^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 = GSE142432
!Series_title = Tissue neutrophil heterogeneity in germ free mice
!Series_geo_accession = GSE142432
!Series_status = Public on Sep 08 2020
!Series_submission_date = Dec 20 2019
!Series_last_update_date = Dec 11 2020
!Series_pubmed_id = 33098771
!Series_summary = Purpose: The goals of this study are to compare bulk RNAseq profiles of tissue neutrophils in germ free mice.
!Series_summary = Methods: Bulk RNAseq of sorted neutrophils from spleen, blood, lung from spf and germ free mice, using Illumina. The sequence reads that passed quality filters were analyzed at the gene level with RSEM.
!Series_overall_design = Examination of different transcriptomic profiles in neutrophils from germ free mice from 3 different tissues.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Iván,,Ballesteros
!Series_contributor = Andrea,,Rubio-Ponce
!Series_contributor = Andrés,,Hidalgo
!Series_sample_id = GSM4227302
!Series_sample_id = GSM4227303
!Series_sample_id = GSM4227304
!Series_sample_id = GSM4227305
!Series_sample_id = GSM4227306
!Series_sample_id = GSM4227307
!Series_sample_id = GSM4227308
!Series_sample_id = GSM4227309
!Series_sample_id = GSM4227310
!Series_sample_id = GSM4227311
!Series_sample_id = GSM4227312
!Series_sample_id = GSM4227313
!Series_sample_id = GSM4227314
!Series_sample_id = GSM4227315
!Series_sample_id = GSM4227316
!Series_sample_id = GSM4227317
!Series_contact_name = Andrés,,Hidalgo
!Series_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Series_contact_institute = Spanish National Center for Cardiovascular Research
!Series_contact_address = Melchor Fernández Almagro, 3
!Series_contact_city = Madrid
!Series_contact_zip/postal_code = 28029
!Series_contact_country = Spain
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE142nnn/GSE142432/suppl/GSE142432_normalized_counts.csv.gz
!Series_platform_id = GPL17021
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = SubSeries of: GSE143255
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA597017
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP238395
^PLATFORM = GPL17021
!Platform_title = Illumina HiSeq 2500 (Mus musculus)
!Platform_geo_accession = GPL17021
!Platform_status = Public on Apr 16 2013
!Platform_submission_date = Apr 16 2013
!Platform_last_update_date = Mar 21 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Mus musculus
!Platform_taxid = 10090
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM4227302
!Sample_title = blood_gf_02
!Sample_geo_accession = GSM4227302
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = blood
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: blood
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Germ-Free mouse
!Sample_description = R02
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656495
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423070
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227303
!Sample_title = blood_gf_03
!Sample_geo_accession = GSM4227303
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = blood
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: blood
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Germ-Free mouse
!Sample_description = R03
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656494
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423071
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227304
!Sample_title = blood_spf_03
!Sample_geo_accession = GSM4227304
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = blood
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: blood
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Specific Pathogen Free mouse
!Sample_description = R07
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656493
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423072
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227305
!Sample_title = blood_spf_04
!Sample_geo_accession = GSM4227305
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = blood
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: blood
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Specific Pathogen Free mouse
!Sample_description = R08
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656492
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423073
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227306
!Sample_title = spleen_gf_01
!Sample_geo_accession = GSM4227306
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = spleen
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Germ-Free mouse
!Sample_description = R09
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656491
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423074
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227307
!Sample_title = spleen_gf_03
!Sample_geo_accession = GSM4227307
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = spleen
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Germ-Free mouse
!Sample_description = R11
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656490
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423075
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227308
!Sample_title = spleen_gf_04
!Sample_geo_accession = GSM4227308
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = spleen
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Germ-Free mouse
!Sample_description = R12
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656489
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423076
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227309
!Sample_title = spleen_spf_01
!Sample_geo_accession = GSM4227309
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = spleen
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Specific Pathogen Free mouse
!Sample_description = R13
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656488
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423077
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227310
!Sample_title = spleen_spf_02
!Sample_geo_accession = GSM4227310
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = spleen
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Specific Pathogen Free mouse
!Sample_description = R14
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656487
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423078
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227311
!Sample_title = spleen_spf_04
!Sample_geo_accession = GSM4227311
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = spleen
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Specific Pathogen Free mouse
!Sample_description = R16
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656486
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423079
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227312
!Sample_title = lung_gf_02
!Sample_geo_accession = GSM4227312
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = lung
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: lung
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Germ-Free mouse
!Sample_description = R18
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656485
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423080
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227313
!Sample_title = lung_gf_03
!Sample_geo_accession = GSM4227313
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = lung
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: lung
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Germ-Free mouse
!Sample_description = R19
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656484
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423081
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227314
!Sample_title = lung_gf_04
!Sample_geo_accession = GSM4227314
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = lung
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: lung
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Germ-Free mouse
!Sample_description = R20
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656483
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423082
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227315
!Sample_title = lung_spf_01
!Sample_geo_accession = GSM4227315
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = lung
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: lung
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Specific Pathogen Free mouse
!Sample_description = R21
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656482
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423083
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227316
!Sample_title = lung_spf_02
!Sample_geo_accession = GSM4227316
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = lung
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: lung
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Specific Pathogen Free mouse
!Sample_description = R22
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656481
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423084
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0
^SAMPLE = GSM4227317
!Sample_title = lung_spf_03
!Sample_geo_accession = GSM4227317
!Sample_status = Public on Sep 08 2020
!Sample_submission_date = Dec 20 2019
!Sample_last_update_date = Sep 08 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = lung
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = cell type: Ly6G+ sorted neutrophils
!Sample_characteristics_ch1 = tissue: lung
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Blood and tissue neutrophils were FACS sorted using CD45, CD11b, Ly6G and DAPI labelling, with typical purities > 95%. RNA was extracted ussing the RNAeasy plus micro kit from QUIAGEN
!Sample_extract_protocol_ch1 = cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using a Quant-iTTM dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and 61 nt long, paired-end reads were generated on a Genome Analyzer IIx, using the TruSeq SBS Kit v5 (Illumina) and following the standard RNA sequencing protocol
!Sample_description = sample obtained from a Specific Pathogen Free mouse
!Sample_description = R23
!Sample_data_processing = Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
!Sample_data_processing = Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
!Sample_data_processing = Counts at gene level were normalized using limma’s (v.3.39.19) voom
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text file include CPM values for each Sample
!Sample_platform_id = GPL17021
!Sample_contact_name = Andrés,,Hidalgo
!Sample_contact_laboratory = Imaging of the Cardiovascular Inflammation and the Immune Response
!Sample_contact_institute = Spanish National Center for Cardiovascular Research
!Sample_contact_address = Melchor Fernández Almagro, 3
!Sample_contact_city = Madrid
!Sample_contact_zip/postal_code = 28029
!Sample_contact_country = Spain
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13656480
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7423085
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE142432
!Sample_series_id = GSE143255
!Sample_data_row_count = 0