^DATABASE = GeoMiame
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
!Database_email = geo@ncbi.nlm.nih.gov
^SERIES = GSE189990
!Series_title = RNA Sequencing in COVID-19 patients identifies neutrophil activation biomarkers as promising diagnostic platform for infections.
!Series_geo_accession = GSE189990
!Series_status = Public on Dec 04 2021
!Series_submission_date = Dec 02 2021
!Series_last_update_date = Dec 04 2021
!Series_summary = Infection with the SARS-CoV2 virus can vary from asymptomatic, flu-like with moderate disease, to critically severe.  Severe disease, termed COVID-19, involves acute respiratory deterioration that is frequently fatal.  To understand the highly variable presentation, and identify biomarkers for disease severity, blood RNA from COVID-19 patient in an intensive care unit was analyzed by whole transcriptome RNA sequencing.  Both SARS-CoV2 infection and the severity of COVID-19 syndrome were associated with up to 25-fold increased expression of neutrophil-related transcripts, such as neutrophil defensin 1 (DEFA1), and 3-5-fold reductions in T cell related transcripts such as the T cell receptor (TCR).  The DEFA1 RNA level detected SARSCoV2 viremia with 95.5% sensitivity, when viremia was measured by ddPCR of whole blood RNA.  Purified CD15+ neutrophils from COVID-19 patients were increased in abundance and showed striking increases in nuclear DNA staining by DAPI.  Concurrently, they showed >10-fold higher elastase activity than normal controls, and correcting for their increased abundance, still showed 5-fold higher elastase activity per cell.  Despite higher CD15+ neutrophil elastase activity, elastase activity was extremely low in plasma from the same patients.  Collectively, the data supports the model that increased neutrophil and decreased T cell activity is associated with increased COVID19 severity, and suggests that blood DEFA1 RNA levels and neutrophil elastase activity, both involved in neutrophil extracellular traps (NETs), may be informative biomarkers of host immune activity after viral infection.
!Series_overall_design = 38 samples from unique COVID-19+ (SARS-CoV-2+) patients and 4 samples from unique healthy control volunteers were analyzed. Of those groups, 20 COVID-19+ samples and 4 healthy control samples underwent RNA sequencing.
!Series_overall_design = NOTE FROM SUBMITTER: We are not submitting raw files because of concern for our patients' privacy.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Richard,S,Wargowsky
!Series_contributor = Philip,,Dela Cruz
!Series_contributor = John,,Lafleur
!Series_contributor = David,,Yamane
!Series_contributor = Justin,,Kim
!Series_contributor = Ivy,,Benjenk
!Series_contributor = Eric,,Heinz
!Series_contributor = Obinna,,Ome Irondi
!Series_contributor = Katherine,,Farrar
!Series_contributor = Ian,,Toma
!Series_contributor = Tristan,,Jordan
!Series_contributor = Jennifer,,Goldman
!Series_contributor = Timothy,,McCaffrey
!Series_sample_id = GSM5710919
!Series_sample_id = GSM5710920
!Series_sample_id = GSM5710921
!Series_sample_id = GSM5710922
!Series_sample_id = GSM5710923
!Series_sample_id = GSM5710924
!Series_sample_id = GSM5710925
!Series_sample_id = GSM5710926
!Series_sample_id = GSM5710927
!Series_sample_id = GSM5710928
!Series_sample_id = GSM5710929
!Series_sample_id = GSM5710930
!Series_sample_id = GSM5710931
!Series_sample_id = GSM5710932
!Series_sample_id = GSM5710933
!Series_sample_id = GSM5710934
!Series_sample_id = GSM5710935
!Series_sample_id = GSM5710936
!Series_sample_id = GSM5710937
!Series_sample_id = GSM5710938
!Series_sample_id = GSM5710939
!Series_sample_id = GSM5710940
!Series_sample_id = GSM5710941
!Series_sample_id = GSM5710942
!Series_contact_name = Timothy,,McCaffrey
!Series_contact_email = mcc@gwu.edu
!Series_contact_laboratory = McCaffrey Transcriptomics Lab
!Series_contact_institute = George Washington University
!Series_contact_address = 2300 I St NW, Ross 203
!Series_contact_city = Washington
!Series_contact_state = DC
!Series_contact_zip/postal_code = 20052
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE189nnn/GSE189990/suppl/GSE189990_COVID_Raw_GX_export_McCaffrey_02DEC2021_V3.xlsx
!Series_platform_id = GPL18573
!Series_platform_taxid = 9606
!Series_sample_taxid = 9606
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA785539
^PLATFORM = GPL18573
!Platform_title = Illumina NextSeq 500 (Homo sapiens)
!Platform_geo_accession = GPL18573
!Platform_status = Public on Apr 15 2014
!Platform_submission_date = Apr 15 2014
!Platform_last_update_date = Mar 26 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Homo sapiens
!Platform_taxid = 9606
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM5710919
!Sample_title = TID001
!Sample_geo_accession = GSM5710919
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 636.7
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575821
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710920
!Sample_title = TID002
!Sample_geo_accession = GSM5710920
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Moderate
!Sample_characteristics_ch1 = covid-19 titer: 6596.1
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575822
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710921
!Sample_title = TID003
!Sample_geo_accession = GSM5710921
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Moderate
!Sample_characteristics_ch1 = covid-19 titer: 18.4
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575823
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710922
!Sample_title = TID005
!Sample_geo_accession = GSM5710922
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 27.7
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: vas
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575824
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710923
!Sample_title = TID006
!Sample_geo_accession = GSM5710923
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: vas
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575825
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710924
!Sample_title = TID007
!Sample_geo_accession = GSM5710924
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 3261.3
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: vas
!Sample_characteristics_ch1 = mortality: fatal
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575826
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710925
!Sample_title = TID008
!Sample_geo_accession = GSM5710925
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 5.4
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: vas
!Sample_characteristics_ch1 = mortality: fatal
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575827
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710926
!Sample_title = TID009
!Sample_geo_accession = GSM5710926
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: vas
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575828
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710927
!Sample_title = TID010
!Sample_geo_accession = GSM5710927
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Incidental
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575829
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710928
!Sample_title = TID011
!Sample_geo_accession = GSM5710928
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Moderate
!Sample_characteristics_ch1 = covid-19 titer: 130.7
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575830
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710929
!Sample_title = TID012
!Sample_geo_accession = GSM5710929
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: vas
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575831
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710930
!Sample_title = TID013
!Sample_geo_accession = GSM5710930
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 5.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: vas
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575832
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710931
!Sample_title = TID014
!Sample_geo_accession = GSM5710931
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 301.5
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: vas
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575833
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710932
!Sample_title = TID015
!Sample_geo_accession = GSM5710932
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Moderate
!Sample_characteristics_ch1 = covid-19 titer: 83.7
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575834
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710933
!Sample_title = TID016
!Sample_geo_accession = GSM5710933
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Incidental
!Sample_characteristics_ch1 = covid-19 titer: 4.8
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575835
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710934
!Sample_title = TID017
!Sample_geo_accession = GSM5710934
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575836
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710935
!Sample_title = TID018
!Sample_geo_accession = GSM5710935
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: fatal
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575837
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710936
!Sample_title = TID019
!Sample_geo_accession = GSM5710936
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 271.8
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: fatal
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575838
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710937
!Sample_title = TID020
!Sample_geo_accession = GSM5710937
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 232.6
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: fatal
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575839
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710938
!Sample_title = TID026
!Sample_geo_accession = GSM5710938
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: Critical
!Sample_characteristics_ch1 = covid-19 titer: 129.3
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: POS
!Sample_characteristics_ch1 = vasopressor: vas
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575840
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710939
!Sample_title = TIC003
!Sample_geo_accession = GSM5710939
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: CONTROL
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575841
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710940
!Sample_title = TIC001
!Sample_geo_accession = GSM5710940
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: CONTROL
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575842
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710941
!Sample_title = TIC004
!Sample_geo_accession = GSM5710941
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: CONTROL
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575843
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0
^SAMPLE = GSM5710942
!Sample_title = TIC005
!Sample_geo_accession = GSM5710942
!Sample_status = Public on Dec 04 2021
!Sample_submission_date = Dec 02 2021
!Sample_last_update_date = Dec 04 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = clinical diagnosis: CONTROL
!Sample_characteristics_ch1 = covid-19 titer: 0.0
!Sample_characteristics_ch1 = covid-19 viremia diagnosis: NEG
!Sample_characteristics_ch1 = vasopressor: no
!Sample_characteristics_ch1 = mortality: ok
!Sample_treatment_protocol_ch1 = 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.
!Sample_growth_protocol_ch1 = Not applicable.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
!Sample_extract_protocol_ch1 = cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
!Sample_extract_protocol_ch1 = RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.
!Sample_data_processing = Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
!Sample_data_processing = Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
!Sample_data_processing = Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.
!Sample_platform_id = GPL18573
!Sample_contact_name = Timothy,,McCaffrey
!Sample_contact_email = mcc@gwu.edu
!Sample_contact_laboratory = McCaffrey Transcriptomics Lab
!Sample_contact_institute = George Washington University
!Sample_contact_address = 2300 I St NW, Ross 203
!Sample_contact_city = Washington
!Sample_contact_state = DC
!Sample_contact_zip/postal_code = 20052
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN23575820
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE189990
!Sample_data_row_count = 0