^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 = GSE185070
!Series_title = Tissue adaptaion of intestinal eosinophils in mice
!Series_geo_accession = GSE185070
!Series_status = Public on Feb 25 2022
!Series_submission_date = Sep 30 2021
!Series_last_update_date = Mar 31 2022
!Series_pubmed_id = 35238865
!Series_summary = To determine how eosinophils adapt to the intestinal environment, eosinophils were sorted from the bone marrow and small intestine and compared by RNA sequencing. We show here that intestinal eosinophils were specifically adapted to their environment and underwent substantial transcriptomic changes. Intestinal eosinophils upregulated genes relating to the immune response and cell-cell communication, extracellular matrix components and metalloproteases, and the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor with broad functions in intestinal homeostasis.
!Series_overall_design = RNA sequencing of eosinophils from two different tissues, bone marrow and small intestine
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Nicola,,Diny
!Series_contributor = Brigitta,,Stockinger
!Series_contributor = Michael,,Shapiro
!Series_sample_id = GSM5605685
!Series_sample_id = GSM5605686
!Series_sample_id = GSM5605687
!Series_sample_id = GSM5605688
!Series_sample_id = GSM5605689
!Series_sample_id = GSM5605690
!Series_sample_id = GSM5605691
!Series_sample_id = GSM5605692
!Series_contact_name = Nicola,Laura,Diny
!Series_contact_institute = The Francis Crick Institute
!Series_contact_address = 1 Midland Rd
!Series_contact_city = London
!Series_contact_zip/postal_code = NW1 1AT
!Series_contact_country = United Kingdom
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE185nnn/GSE185070/suppl/GSE185070_SIvsBM_varianceStabilizedExpression.txt.gz
!Series_platform_id = GPL21103
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA767596
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP339489
^PLATFORM = GPL21103
!Platform_title = Illumina HiSeq 4000 (Mus musculus)
!Platform_geo_accession = GPL21103
!Platform_status = Public on Nov 04 2015
!Platform_submission_date = Nov 04 2015
!Platform_last_update_date = Mar 19 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 = GSM5605685
!Sample_title = bone marrow eosinophils_WT_F1
!Sample_geo_accession = GSM5605685
!Sample_status = Public on Feb 25 2022
!Sample_submission_date = Sep 30 2021
!Sample_last_update_date = Feb 25 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow eosinophils
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57/BL6
!Sample_characteristics_ch1 = genotype: wildtype
!Sample_characteristics_ch1 = tissue: bone marrow
!Sample_characteristics_ch1 = cell type: eosinophils
!Sample_characteristics_ch1 = cell population: CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils
!Sample_treatment_protocol_ch1 = cells were immediately processed for RNA isolation
!Sample_growth_protocol_ch1 = Eosinophils were FACS-sorted from the intestine (CD11b+MHC-II-SiglecF+SSChi eosinophils) or bone marrow (CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils)
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRI Reagent and the RiboPure RNA Purification Kit (ThermoFisher Scientific #AM1924) immediately after sorting. RNA quality and quantity was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Pico Kit. Only samples with RIN ≥7 were used for RNA sequencing.
!Sample_extract_protocol_ch1 = RNA samples were converted into cDNA using the NuGEN Ovation RNA-Seq System v2. Illumina-compatible libraries were produced using the NuGEN Ovation Ultralow Library System V2.  Sequencing was performed on the Illumina HiSeq 4000 with single ended reads of at least 75 bp.
!Sample_description = DIN1007A20
!Sample_data_processing = Fastq files were aligned to the GRCm38 Ensembl Release 86 mouse genome using the nextflow package nf-core/rnaseq to generate gene counts.
!Sample_data_processing = Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). We recorded as differentially expressed those genes with adjusted p values < 0.05.
!Sample_data_processing = We also relied on DESeq2 for PCA of variance stabilized expression values.
!Sample_data_processing = All computations were performed in R version 4.0.3 (2020-10-10).
!Sample_data_processing = Genome_build: GRCm38 Ensembl Release 86 mouse genome
!Sample_data_processing = Supplementary_files_format_and_content: Tab delimited text file containing variance stabilized counts for each sample and each gene
!Sample_platform_id = GPL21103
!Sample_contact_name = Nicola,Laura,Diny
!Sample_contact_institute = The Francis Crick Institute
!Sample_contact_address = 1 Midland Rd
!Sample_contact_city = London
!Sample_contact_zip/postal_code = NW1 1AT
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN21911382
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX12414429
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE185070
!Sample_data_row_count = 0
^SAMPLE = GSM5605686
!Sample_title = bone marrow eosinophils_WT_F2
!Sample_geo_accession = GSM5605686
!Sample_status = Public on Feb 25 2022
!Sample_submission_date = Sep 30 2021
!Sample_last_update_date = Feb 25 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow eosinophils
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57/BL6
!Sample_characteristics_ch1 = genotype: wildtype
!Sample_characteristics_ch1 = tissue: bone marrow
!Sample_characteristics_ch1 = cell type: eosinophils
!Sample_characteristics_ch1 = cell population: CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils
!Sample_treatment_protocol_ch1 = cells were immediately processed for RNA isolation
!Sample_growth_protocol_ch1 = Eosinophils were FACS-sorted from the intestine (CD11b+MHC-II-SiglecF+SSChi eosinophils) or bone marrow (CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils)
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRI Reagent and the RiboPure RNA Purification Kit (ThermoFisher Scientific #AM1924) immediately after sorting. RNA quality and quantity was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Pico Kit. Only samples with RIN ≥7 were used for RNA sequencing.
!Sample_extract_protocol_ch1 = RNA samples were converted into cDNA using the NuGEN Ovation RNA-Seq System v2. Illumina-compatible libraries were produced using the NuGEN Ovation Ultralow Library System V2.  Sequencing was performed on the Illumina HiSeq 4000 with single ended reads of at least 75 bp.
!Sample_description = DIN1007A22
!Sample_data_processing = Fastq files were aligned to the GRCm38 Ensembl Release 86 mouse genome using the nextflow package nf-core/rnaseq to generate gene counts.
!Sample_data_processing = Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). We recorded as differentially expressed those genes with adjusted p values < 0.05.
!Sample_data_processing = We also relied on DESeq2 for PCA of variance stabilized expression values.
!Sample_data_processing = All computations were performed in R version 4.0.3 (2020-10-10).
!Sample_data_processing = Genome_build: GRCm38 Ensembl Release 86 mouse genome
!Sample_data_processing = Supplementary_files_format_and_content: Tab delimited text file containing variance stabilized counts for each sample and each gene
!Sample_platform_id = GPL21103
!Sample_contact_name = Nicola,Laura,Diny
!Sample_contact_institute = The Francis Crick Institute
!Sample_contact_address = 1 Midland Rd
!Sample_contact_city = London
!Sample_contact_zip/postal_code = NW1 1AT
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN21911381
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX12414430
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE185070
!Sample_data_row_count = 0
^SAMPLE = GSM5605687
!Sample_title = bone marrow eosinophils_WT_F3
!Sample_geo_accession = GSM5605687
!Sample_status = Public on Feb 25 2022
!Sample_submission_date = Sep 30 2021
!Sample_last_update_date = Feb 25 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow eosinophils
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57/BL6
!Sample_characteristics_ch1 = genotype: wildtype
!Sample_characteristics_ch1 = tissue: bone marrow
!Sample_characteristics_ch1 = cell type: eosinophils
!Sample_characteristics_ch1 = cell population: CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils
!Sample_treatment_protocol_ch1 = cells were immediately processed for RNA isolation
!Sample_growth_protocol_ch1 = Eosinophils were FACS-sorted from the intestine (CD11b+MHC-II-SiglecF+SSChi eosinophils) or bone marrow (CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils)
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRI Reagent and the RiboPure RNA Purification Kit (ThermoFisher Scientific #AM1924) immediately after sorting. RNA quality and quantity was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Pico Kit. Only samples with RIN ≥7 were used for RNA sequencing.
!Sample_extract_protocol_ch1 = RNA samples were converted into cDNA using the NuGEN Ovation RNA-Seq System v2. Illumina-compatible libraries were produced using the NuGEN Ovation Ultralow Library System V2.  Sequencing was performed on the Illumina HiSeq 4000 with single ended reads of at least 75 bp.
!Sample_description = DIN1007A23
!Sample_data_processing = Fastq files were aligned to the GRCm38 Ensembl Release 86 mouse genome using the nextflow package nf-core/rnaseq to generate gene counts.
!Sample_data_processing = Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). We recorded as differentially expressed those genes with adjusted p values < 0.05.
!Sample_data_processing = We also relied on DESeq2 for PCA of variance stabilized expression values.
!Sample_data_processing = All computations were performed in R version 4.0.3 (2020-10-10).
!Sample_data_processing = Genome_build: GRCm38 Ensembl Release 86 mouse genome
!Sample_data_processing = Supplementary_files_format_and_content: Tab delimited text file containing variance stabilized counts for each sample and each gene
!Sample_platform_id = GPL21103
!Sample_contact_name = Nicola,Laura,Diny
!Sample_contact_institute = The Francis Crick Institute
!Sample_contact_address = 1 Midland Rd
!Sample_contact_city = London
!Sample_contact_zip/postal_code = NW1 1AT
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN21911380
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX12414431
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE185070
!Sample_data_row_count = 0
^SAMPLE = GSM5605688
!Sample_title = bone marrow eosinophils_WT_F4
!Sample_geo_accession = GSM5605688
!Sample_status = Public on Feb 25 2022
!Sample_submission_date = Sep 30 2021
!Sample_last_update_date = Feb 25 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow eosinophils
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57/BL6
!Sample_characteristics_ch1 = genotype: wildtype
!Sample_characteristics_ch1 = tissue: bone marrow
!Sample_characteristics_ch1 = cell type: eosinophils
!Sample_characteristics_ch1 = cell population: CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils
!Sample_treatment_protocol_ch1 = cells were immediately processed for RNA isolation
!Sample_growth_protocol_ch1 = Eosinophils were FACS-sorted from the intestine (CD11b+MHC-II-SiglecF+SSChi eosinophils) or bone marrow (CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils)
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRI Reagent and the RiboPure RNA Purification Kit (ThermoFisher Scientific #AM1924) immediately after sorting. RNA quality and quantity was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Pico Kit. Only samples with RIN ≥7 were used for RNA sequencing.
!Sample_extract_protocol_ch1 = RNA samples were converted into cDNA using the NuGEN Ovation RNA-Seq System v2. Illumina-compatible libraries were produced using the NuGEN Ovation Ultralow Library System V2.  Sequencing was performed on the Illumina HiSeq 4000 with single ended reads of at least 75 bp.
!Sample_description = DIN1007A24
!Sample_data_processing = Fastq files were aligned to the GRCm38 Ensembl Release 86 mouse genome using the nextflow package nf-core/rnaseq to generate gene counts.
!Sample_data_processing = Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). We recorded as differentially expressed those genes with adjusted p values < 0.05.
!Sample_data_processing = We also relied on DESeq2 for PCA of variance stabilized expression values.
!Sample_data_processing = All computations were performed in R version 4.0.3 (2020-10-10).
!Sample_data_processing = Genome_build: GRCm38 Ensembl Release 86 mouse genome
!Sample_data_processing = Supplementary_files_format_and_content: Tab delimited text file containing variance stabilized counts for each sample and each gene
!Sample_platform_id = GPL21103
!Sample_contact_name = Nicola,Laura,Diny
!Sample_contact_institute = The Francis Crick Institute
!Sample_contact_address = 1 Midland Rd
!Sample_contact_city = London
!Sample_contact_zip/postal_code = NW1 1AT
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN21911379
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX12414432
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE185070
!Sample_data_row_count = 0
^SAMPLE = GSM5605689
!Sample_title = small intestinal eosinophils_WT_F5
!Sample_geo_accession = GSM5605689
!Sample_status = Public on Feb 25 2022
!Sample_submission_date = Sep 30 2021
!Sample_last_update_date = Feb 25 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = small intestinal eosinophils
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57/BL6
!Sample_characteristics_ch1 = genotype: wildtype
!Sample_characteristics_ch1 = tissue: small intestine
!Sample_characteristics_ch1 = cell type: eosinophils
!Sample_characteristics_ch1 = cell population: CD11b+MHC-II-SiglecF+SSChi eosinophils
!Sample_treatment_protocol_ch1 = cells were immediately processed for RNA isolation
!Sample_growth_protocol_ch1 = Eosinophils were FACS-sorted from the intestine (CD11b+MHC-II-SiglecF+SSChi eosinophils) or bone marrow (CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils)
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRI Reagent and the RiboPure RNA Purification Kit (ThermoFisher Scientific #AM1924) immediately after sorting. RNA quality and quantity was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Pico Kit. Only samples with RIN ≥7 were used for RNA sequencing.
!Sample_extract_protocol_ch1 = RNA samples were converted into cDNA using the NuGEN Ovation RNA-Seq System v2. Illumina-compatible libraries were produced using the NuGEN Ovation Ultralow Library System V2.  Sequencing was performed on the Illumina HiSeq 4000 with single ended reads of at least 75 bp.
!Sample_description = DIN1007A5
!Sample_data_processing = Fastq files were aligned to the GRCm38 Ensembl Release 86 mouse genome using the nextflow package nf-core/rnaseq to generate gene counts.
!Sample_data_processing = Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). We recorded as differentially expressed those genes with adjusted p values < 0.05.
!Sample_data_processing = We also relied on DESeq2 for PCA of variance stabilized expression values.
!Sample_data_processing = All computations were performed in R version 4.0.3 (2020-10-10).
!Sample_data_processing = Genome_build: GRCm38 Ensembl Release 86 mouse genome
!Sample_data_processing = Supplementary_files_format_and_content: Tab delimited text file containing variance stabilized counts for each sample and each gene
!Sample_platform_id = GPL21103
!Sample_contact_name = Nicola,Laura,Diny
!Sample_contact_institute = The Francis Crick Institute
!Sample_contact_address = 1 Midland Rd
!Sample_contact_city = London
!Sample_contact_zip/postal_code = NW1 1AT
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN21911378
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX12414433
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE185070
!Sample_data_row_count = 0
^SAMPLE = GSM5605690
!Sample_title = small intestinal eosinophils_WT_F6
!Sample_geo_accession = GSM5605690
!Sample_status = Public on Feb 25 2022
!Sample_submission_date = Sep 30 2021
!Sample_last_update_date = Feb 25 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = small intestinal eosinophils
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57/BL6
!Sample_characteristics_ch1 = genotype: wildtype
!Sample_characteristics_ch1 = tissue: small intestine
!Sample_characteristics_ch1 = cell type: eosinophils
!Sample_characteristics_ch1 = cell population: CD11b+MHC-II-SiglecF+SSChi eosinophils
!Sample_treatment_protocol_ch1 = cells were immediately processed for RNA isolation
!Sample_growth_protocol_ch1 = Eosinophils were FACS-sorted from the intestine (CD11b+MHC-II-SiglecF+SSChi eosinophils) or bone marrow (CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils)
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRI Reagent and the RiboPure RNA Purification Kit (ThermoFisher Scientific #AM1924) immediately after sorting. RNA quality and quantity was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Pico Kit. Only samples with RIN ≥7 were used for RNA sequencing.
!Sample_extract_protocol_ch1 = RNA samples were converted into cDNA using the NuGEN Ovation RNA-Seq System v2. Illumina-compatible libraries were produced using the NuGEN Ovation Ultralow Library System V2.  Sequencing was performed on the Illumina HiSeq 4000 with single ended reads of at least 75 bp.
!Sample_description = DIN1007A6
!Sample_data_processing = Fastq files were aligned to the GRCm38 Ensembl Release 86 mouse genome using the nextflow package nf-core/rnaseq to generate gene counts.
!Sample_data_processing = Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). We recorded as differentially expressed those genes with adjusted p values < 0.05.
!Sample_data_processing = We also relied on DESeq2 for PCA of variance stabilized expression values.
!Sample_data_processing = All computations were performed in R version 4.0.3 (2020-10-10).
!Sample_data_processing = Genome_build: GRCm38 Ensembl Release 86 mouse genome
!Sample_data_processing = Supplementary_files_format_and_content: Tab delimited text file containing variance stabilized counts for each sample and each gene
!Sample_platform_id = GPL21103
!Sample_contact_name = Nicola,Laura,Diny
!Sample_contact_institute = The Francis Crick Institute
!Sample_contact_address = 1 Midland Rd
!Sample_contact_city = London
!Sample_contact_zip/postal_code = NW1 1AT
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN21911377
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX12414434
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE185070
!Sample_data_row_count = 0
^SAMPLE = GSM5605691
!Sample_title = small intestinal eosinophils_WT_F7
!Sample_geo_accession = GSM5605691
!Sample_status = Public on Feb 25 2022
!Sample_submission_date = Sep 30 2021
!Sample_last_update_date = Feb 25 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = small intestinal eosinophils
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57/BL6
!Sample_characteristics_ch1 = genotype: wildtype
!Sample_characteristics_ch1 = tissue: small intestine
!Sample_characteristics_ch1 = cell type: eosinophils
!Sample_characteristics_ch1 = cell population: CD11b+MHC-II-SiglecF+SSChi eosinophils
!Sample_treatment_protocol_ch1 = cells were immediately processed for RNA isolation
!Sample_growth_protocol_ch1 = Eosinophils were FACS-sorted from the intestine (CD11b+MHC-II-SiglecF+SSChi eosinophils) or bone marrow (CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils)
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRI Reagent and the RiboPure RNA Purification Kit (ThermoFisher Scientific #AM1924) immediately after sorting. RNA quality and quantity was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Pico Kit. Only samples with RIN ≥7 were used for RNA sequencing.
!Sample_extract_protocol_ch1 = RNA samples were converted into cDNA using the NuGEN Ovation RNA-Seq System v2. Illumina-compatible libraries were produced using the NuGEN Ovation Ultralow Library System V2.  Sequencing was performed on the Illumina HiSeq 4000 with single ended reads of at least 75 bp.
!Sample_description = DIN1007A17
!Sample_data_processing = Fastq files were aligned to the GRCm38 Ensembl Release 86 mouse genome using the nextflow package nf-core/rnaseq to generate gene counts.
!Sample_data_processing = Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). We recorded as differentially expressed those genes with adjusted p values < 0.05.
!Sample_data_processing = We also relied on DESeq2 for PCA of variance stabilized expression values.
!Sample_data_processing = All computations were performed in R version 4.0.3 (2020-10-10).
!Sample_data_processing = Genome_build: GRCm38 Ensembl Release 86 mouse genome
!Sample_data_processing = Supplementary_files_format_and_content: Tab delimited text file containing variance stabilized counts for each sample and each gene
!Sample_platform_id = GPL21103
!Sample_contact_name = Nicola,Laura,Diny
!Sample_contact_institute = The Francis Crick Institute
!Sample_contact_address = 1 Midland Rd
!Sample_contact_city = London
!Sample_contact_zip/postal_code = NW1 1AT
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN21911376
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX12414435
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE185070
!Sample_data_row_count = 0
^SAMPLE = GSM5605692
!Sample_title = small intestinal eosinophils_WT_F8
!Sample_geo_accession = GSM5605692
!Sample_status = Public on Feb 25 2022
!Sample_submission_date = Sep 30 2021
!Sample_last_update_date = Feb 25 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = small intestinal eosinophils
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57/BL6
!Sample_characteristics_ch1 = genotype: wildtype
!Sample_characteristics_ch1 = tissue: small intestine
!Sample_characteristics_ch1 = cell type: eosinophils
!Sample_characteristics_ch1 = cell population: CD11b+MHC-II-SiglecF+SSChi eosinophils
!Sample_treatment_protocol_ch1 = cells were immediately processed for RNA isolation
!Sample_growth_protocol_ch1 = Eosinophils were FACS-sorted from the intestine (CD11b+MHC-II-SiglecF+SSChi eosinophils) or bone marrow (CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils)
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRI Reagent and the RiboPure RNA Purification Kit (ThermoFisher Scientific #AM1924) immediately after sorting. RNA quality and quantity was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Pico Kit. Only samples with RIN ≥7 were used for RNA sequencing.
!Sample_extract_protocol_ch1 = RNA samples were converted into cDNA using the NuGEN Ovation RNA-Seq System v2. Illumina-compatible libraries were produced using the NuGEN Ovation Ultralow Library System V2.  Sequencing was performed on the Illumina HiSeq 4000 with single ended reads of at least 75 bp.
!Sample_description = DIN1007A18
!Sample_data_processing = Fastq files were aligned to the GRCm38 Ensembl Release 86 mouse genome using the nextflow package nf-core/rnaseq to generate gene counts.
!Sample_data_processing = Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). We recorded as differentially expressed those genes with adjusted p values < 0.05.
!Sample_data_processing = We also relied on DESeq2 for PCA of variance stabilized expression values.
!Sample_data_processing = All computations were performed in R version 4.0.3 (2020-10-10).
!Sample_data_processing = Genome_build: GRCm38 Ensembl Release 86 mouse genome
!Sample_data_processing = Supplementary_files_format_and_content: Tab delimited text file containing variance stabilized counts for each sample and each gene
!Sample_platform_id = GPL21103
!Sample_contact_name = Nicola,Laura,Diny
!Sample_contact_institute = The Francis Crick Institute
!Sample_contact_address = 1 Midland Rd
!Sample_contact_city = London
!Sample_contact_zip/postal_code = NW1 1AT
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN21911375
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX12414436
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE185070
!Sample_data_row_count = 0