^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 = GSE202108
!Series_title = RNA-seq analysis of bead-purified B cells of 5-week-old TLR9-/- MRL/lpr mice stimulated in vitro with TLR7 agonists (CL097, invivogen) or left unstimulated.
!Series_geo_accession = GSE202108
!Series_status = Public on Aug 03 2022
!Series_submission_date = May 03 2022
!Series_last_update_date = Aug 06 2022
!Series_summary = Purpose: The goal of this study was to develop a B-cell specific gene signature to catalog induced genes after short term in vitro TLR7 stimulation of TLR9-/- MRL/lpr B cells.
!Series_summary = Methods : Bead purified B cells (5M) from three 5-week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated. RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN). Samples were sequenced on an NextSeq500 (Illumina, Inc) with 2 x 75 bp paired-end reads (20 million reads per sample).
!Series_summary = Results: a B-cell specific gene signature of induced genes after short term in vitro TLR7 stimulation was cataloged.
!Series_overall_design = mRNA profiles of TLR9 deficient (TLR9-/-) B cells stimulated in vitro with TLR7 agonists (CL097, Invivogen) or unstimulated, were generated in three replicates, by sequencing on an Illumina NextSeq500 using PE 150 Cycles High Output flowcell.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Claire,,Leibler
!Series_contributor = Shuchi,,Smita
!Series_contributor = Mark,J,Shlomchik
!Series_sample_id = GSM6094646
!Series_sample_id = GSM6094647
!Series_sample_id = GSM6094648
!Series_sample_id = GSM6094649
!Series_sample_id = GSM6094650
!Series_sample_id = GSM6094651
!Series_contact_name = Mark,,Shlomchik
!Series_contact_email = shlomchiklab@gmail.com
!Series_contact_laboratory = W1052 Biomedical Science Tower
!Series_contact_department = Department of Immunology
!Series_contact_institute = University of Pittsburgh
!Series_contact_address = 200 Lothrop street
!Series_contact_city = Pittsburgh
!Series_contact_state = PA
!Series_contact_zip/postal_code = 15261
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE202nnn/GSE202108/suppl/GSE202108_RAW.tar
!Series_platform_id = GPL24247
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA834733
^PLATFORM = GPL24247
!Platform_title = Illumina NovaSeq 6000 (Mus musculus)
!Platform_geo_accession = GPL24247
!Platform_status = Public on Nov 08 2017
!Platform_submission_date = Nov 08 2017
!Platform_last_update_date = Mar 08 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 = GSM6094646
!Sample_title = TLR9KO_TLR7WT_stimNo.1
!Sample_geo_accession = GSM6094646
!Sample_status = Public on Aug 03 2022
!Sample_submission_date = May 03 2022
!Sample_last_update_date = Aug 04 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = B cells_TLR9-/- MRL/lpr_unstimulated _Rep1
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: MRL/lpr (MRL.Faslpr)
!Sample_characteristics_ch1 = tissue: Bead purified B cells
!Sample_characteristics_ch1 = cell type: B cells
!Sample_treatment_protocol_ch1 = Bead purified B cells (5M) from three 5-7week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA  for Sequencing.
!Sample_data_processing = Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
!Sample_data_processing = Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
!Sample_data_processing = The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
!Sample_data_processing = Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
!Sample_data_processing = Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
!Sample_data_processing = Assembly: Mus musculus reference genome (mm10).
!Sample_data_processing = Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Mark,,Shlomchik
!Sample_contact_email = shlomchiklab@gmail.com
!Sample_contact_laboratory = W1052 Biomedical Science Tower
!Sample_contact_department = Department of Immunology
!Sample_contact_institute = University of Pittsburgh
!Sample_contact_address = 200 Lothrop street
!Sample_contact_city = Pittsburgh
!Sample_contact_state = PA
!Sample_contact_zip/postal_code = 15261
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN28055442
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX15123960
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6094nnn/GSM6094646/suppl/GSM6094646_TLR9KO_TLR7WT_stimNo.1.txt.gz
!Sample_series_id = GSE202108
!Sample_data_row_count = 0
^SAMPLE = GSM6094647
!Sample_title = TLR9KO_TLR7WT_stimNo.2
!Sample_geo_accession = GSM6094647
!Sample_status = Public on Aug 03 2022
!Sample_submission_date = May 03 2022
!Sample_last_update_date = Aug 04 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = B cells_TLR9-/- MRL/lpr_unstimulated _Rep2
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: MRL/lpr (MRL.Faslpr)
!Sample_characteristics_ch1 = tissue: Bead purified B cells
!Sample_characteristics_ch1 = cell type: B cells
!Sample_treatment_protocol_ch1 = Bead purified B cells (5M) from three 5-7week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA  for Sequencing.
!Sample_data_processing = Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
!Sample_data_processing = Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
!Sample_data_processing = The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
!Sample_data_processing = Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
!Sample_data_processing = Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
!Sample_data_processing = Assembly: Mus musculus reference genome (mm10).
!Sample_data_processing = Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Mark,,Shlomchik
!Sample_contact_email = shlomchiklab@gmail.com
!Sample_contact_laboratory = W1052 Biomedical Science Tower
!Sample_contact_department = Department of Immunology
!Sample_contact_institute = University of Pittsburgh
!Sample_contact_address = 200 Lothrop street
!Sample_contact_city = Pittsburgh
!Sample_contact_state = PA
!Sample_contact_zip/postal_code = 15261
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN28055441
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX15123961
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6094nnn/GSM6094647/suppl/GSM6094647_TLR9KO_TLR7WT_stimNo.2.txt.gz
!Sample_series_id = GSE202108
!Sample_data_row_count = 0
^SAMPLE = GSM6094648
!Sample_title = TLR9KO_TLR7WT_stimNo.3
!Sample_geo_accession = GSM6094648
!Sample_status = Public on Aug 03 2022
!Sample_submission_date = May 03 2022
!Sample_last_update_date = Aug 04 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = B cells_TLR9-/- MRL/lpr_unstimulated _Rep3
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: MRL/lpr (MRL.Faslpr)
!Sample_characteristics_ch1 = tissue: Bead purified B cells
!Sample_characteristics_ch1 = cell type: B cells
!Sample_treatment_protocol_ch1 = Bead purified B cells (5M) from three 5-7week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA  for Sequencing.
!Sample_data_processing = Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
!Sample_data_processing = Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
!Sample_data_processing = The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
!Sample_data_processing = Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
!Sample_data_processing = Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
!Sample_data_processing = Assembly: Mus musculus reference genome (mm10).
!Sample_data_processing = Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Mark,,Shlomchik
!Sample_contact_email = shlomchiklab@gmail.com
!Sample_contact_laboratory = W1052 Biomedical Science Tower
!Sample_contact_department = Department of Immunology
!Sample_contact_institute = University of Pittsburgh
!Sample_contact_address = 200 Lothrop street
!Sample_contact_city = Pittsburgh
!Sample_contact_state = PA
!Sample_contact_zip/postal_code = 15261
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN28055440
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX15123962
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6094nnn/GSM6094648/suppl/GSM6094648_TLR9KO_TLR7WT_stimNo.3.txt.gz
!Sample_series_id = GSE202108
!Sample_data_row_count = 0
^SAMPLE = GSM6094649
!Sample_title = TLR9KO_TLR7WT_stimTLR7.1
!Sample_geo_accession = GSM6094649
!Sample_status = Public on Aug 03 2022
!Sample_submission_date = May 03 2022
!Sample_last_update_date = Aug 04 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = B cells_TLR9-/- MRL/lpr_stimulated with TLR7 agonist (CL097)_Rep1
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: MRL/lpr (MRL.Faslpr)
!Sample_characteristics_ch1 = tissue: Bead purified B cells
!Sample_characteristics_ch1 = cell type: B cells
!Sample_treatment_protocol_ch1 = Bead purified B cells (5M) from three 5-7week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA  for Sequencing.
!Sample_data_processing = Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
!Sample_data_processing = Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
!Sample_data_processing = The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
!Sample_data_processing = Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
!Sample_data_processing = Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
!Sample_data_processing = Assembly: Mus musculus reference genome (mm10).
!Sample_data_processing = Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Mark,,Shlomchik
!Sample_contact_email = shlomchiklab@gmail.com
!Sample_contact_laboratory = W1052 Biomedical Science Tower
!Sample_contact_department = Department of Immunology
!Sample_contact_institute = University of Pittsburgh
!Sample_contact_address = 200 Lothrop street
!Sample_contact_city = Pittsburgh
!Sample_contact_state = PA
!Sample_contact_zip/postal_code = 15261
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN28055439
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX15123963
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6094nnn/GSM6094649/suppl/GSM6094649_TLR9KO_TLR7WT_stimTLR7.1.txt.gz
!Sample_series_id = GSE202108
!Sample_data_row_count = 0
^SAMPLE = GSM6094650
!Sample_title = TLR9KO_TLR7WT_stimTLR7.2
!Sample_geo_accession = GSM6094650
!Sample_status = Public on Aug 03 2022
!Sample_submission_date = May 03 2022
!Sample_last_update_date = Aug 04 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = B cells_TLR9-/- MRL/lpr_stimulated with TLR7 agonist (CL097)_Rep2
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: MRL/lpr (MRL.Faslpr)
!Sample_characteristics_ch1 = tissue: Bead purified B cells
!Sample_characteristics_ch1 = cell type: B cells
!Sample_treatment_protocol_ch1 = Bead purified B cells (5M) from three 5-7week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA  for Sequencing.
!Sample_data_processing = Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
!Sample_data_processing = Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
!Sample_data_processing = The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
!Sample_data_processing = Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
!Sample_data_processing = Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
!Sample_data_processing = Assembly: Mus musculus reference genome (mm10).
!Sample_data_processing = Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Mark,,Shlomchik
!Sample_contact_email = shlomchiklab@gmail.com
!Sample_contact_laboratory = W1052 Biomedical Science Tower
!Sample_contact_department = Department of Immunology
!Sample_contact_institute = University of Pittsburgh
!Sample_contact_address = 200 Lothrop street
!Sample_contact_city = Pittsburgh
!Sample_contact_state = PA
!Sample_contact_zip/postal_code = 15261
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN28055438
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX15123964
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6094nnn/GSM6094650/suppl/GSM6094650_TLR9KO_TLR7WT_stimTLR7.2.txt.gz
!Sample_series_id = GSE202108
!Sample_data_row_count = 0
^SAMPLE = GSM6094651
!Sample_title = TLR9KO_TLR7WT_stimTLR7.3
!Sample_geo_accession = GSM6094651
!Sample_status = Public on Aug 03 2022
!Sample_submission_date = May 03 2022
!Sample_last_update_date = Aug 04 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = B cells_TLR9-/- MRL/lpr_stimulated with TLR7 agonist (CL097)_Rep3
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: spleen
!Sample_characteristics_ch1 = strain: MRL/lpr (MRL.Faslpr)
!Sample_characteristics_ch1 = tissue: Bead purified B cells
!Sample_characteristics_ch1 = cell type: B cells
!Sample_treatment_protocol_ch1 = Bead purified B cells (5M) from three 5-7week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA  for Sequencing.
!Sample_data_processing = Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
!Sample_data_processing = Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
!Sample_data_processing = The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
!Sample_data_processing = Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
!Sample_data_processing = Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
!Sample_data_processing = Assembly: Mus musculus reference genome (mm10).
!Sample_data_processing = Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Mark,,Shlomchik
!Sample_contact_email = shlomchiklab@gmail.com
!Sample_contact_laboratory = W1052 Biomedical Science Tower
!Sample_contact_department = Department of Immunology
!Sample_contact_institute = University of Pittsburgh
!Sample_contact_address = 200 Lothrop street
!Sample_contact_city = Pittsburgh
!Sample_contact_state = PA
!Sample_contact_zip/postal_code = 15261
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN28055437
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX15123965
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6094nnn/GSM6094651/suppl/GSM6094651_TLR9KO_TLR7WT_stimTLR7.3.txt.gz
!Sample_series_id = GSE202108
!Sample_data_row_count = 0