^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 = GSE153632
!Series_title = Regulatory eosinophils triggered by innate lymphoid cells type 2 during asthma induce resolution of chronic arthritis
!Series_geo_accession = GSE153632
!Series_status = Public on Nov 12 2020
!Series_submission_date = Jul 01 2020
!Series_last_update_date = Nov 12 2020
!Series_summary = Eosinophils possess distinct functions, being pro-inflammatory in asthma and worm infection on the one hand, while supporting resolution of inflammation and tissue repair on the other hand. We could demonstrate that the immunological pathways causing asthma in the lungs at the same time elicit resolution of arthritis in the joints in an eosinophil-dependent manner. It can be hypothesized that the pro-inflammatory action of eosinophils in the lungs and their homeostatic functions in the synovium are mediated by tissue-specific functional priming. Therefore, single cell RNA sequencing (scRNA-seq) was used to investigate whether distinct eosinophil subsets arise in the lungs and the joints of mice upon combined asthma/arthritis model.
!Series_overall_design = Single cell mRNA sequencing of sorted CD45+CD11b+Sigec-F+ granulocytes of lung and synovial tissue from mice with eosinophilic asthma (OVA), K/BxN serum-induced arthritis (SIA) and a comination of asthma and arthritis (OVA+SIA) at day 7 post-SIA
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Aline,,Bozec
!Series_contributor = Darja,,Andreev
!Series_contributor = Mengdan,,Liu
!Series_contributor = Philipp,,Kirchner
!Series_contributor = Arif,B,Ekici
!Series_sample_id = GSM4648437
!Series_sample_id = GSM4648438
!Series_sample_id = GSM4648439
!Series_contact_name = Philipp,,Kirchner
!Series_contact_department = Institute of Human Genetics
!Series_contact_institute = University Hospital Friedrich Alexander Universitaet Erlangen-Nuernberg
!Series_contact_address = Schwabachanlage 10
!Series_contact_city = Erlangen
!Series_contact_zip/postal_code = 91054
!Series_contact_country = Germany
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153632/suppl/GSE153632_RAW.tar
!Series_platform_id = GPL17021
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA643518
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP269549
^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 = GSM4648437
!Sample_title = Lung_OVA+SIA
!Sample_geo_accession = GSM4648437
!Sample_status = Public on Nov 12 2020
!Sample_submission_date = Jul 01 2020
!Sample_last_update_date = Nov 12 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Lung eosinophil granulocytes
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Lung tissue
!Sample_characteristics_ch1 = strain: Balb/c
!Sample_characteristics_ch1 = cell type: CD45+CD11b+Siglec-F+ granulocytes
!Sample_characteristics_ch1 = treatment: OVA+SIA
!Sample_characteristics_ch1 = time point: Day 7 post SIA
!Sample_treatment_protocol_ch1 = To trigger eosinophilic asthma, 6 weeks old Balb/c mice were sensitized twice with intraperitoneal injection of 100µg OVA/Alum mixture at day -20 and -13, and challenged three times with intranasal injection of 50µg OVA at day -2, -1 and 0. At day 0, mice were injected with 150µl K/BxN serum intraperitoneally for inducing SIA. Mice were challenged again at day 4, 5, 6 with intranasal injection of 50µg OVA and sacrificed at day 7.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The  lungs of 3 mice were pooled for the sample Lung_OVA+SIA, 16 hind ankle joints (8 mice) were pooled for the sample Synovium_OVA+SIA and 24 hind ankle joints (12 mice) were pooled for the sample Synovium_SIA. Eosinophils were sorted via the markers CD45+ CD11b+ Siglec-F+. For each sample 8000 cells were loaded onto a Chromium Single Cell A Chip (10x Genomics) with Chromium Single Cell 3' v3 Gel Beads (10x Genomics) to generate single cell bead emulsions for reverse transcription and cell bar coding according to the manufacturers instructions
!Sample_extract_protocol_ch1 = Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v3 and i7 Mutiplex kit (10X Genomics) according to the manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2500 using the recommended read lengths for Chromium Single Cell 3' v3 chemistry.
!Sample_data_processing = Illumina RTA 1.18.66.3 was used for base calling
!Sample_data_processing = Base calling files were converted to FASTQ files and demultiplexed using Cell Ranger v3.0.1 (10x Genomics) mkfastq with standard parameters.
!Sample_data_processing = Cell Ranger v3.0.1 quant was used to map the demultiplexed reads to the reference genome (mm10, v3.0.0, 10x Genomics), process cell barcodes, generate expression matrices of UMI (unique molecule identifier) counts per droplet and estimate the number of cells using standard parameters.
!Sample_data_processing = Seurat v3.1.0 was used under R v3.6.1 to first remove low quality cells expressing less than 300 genes or more than 20% mitochondrial genes or both. The filtered cells were clustered by similarity in gene expression and visualized. For the clusters marker genes were determined.
!Sample_data_processing = To compare between tissues, data sets were integrated follwing the recommended approach for SCT-transformed data in Seurat v3.1.0
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: tab delimited text files with UMI counts per gene per cell after filtering in Seurat (min.cells = 3, min.genes = 300)
!Sample_platform_id = GPL17021
!Sample_contact_name = Philipp,,Kirchner
!Sample_contact_department = Institute of Human Genetics
!Sample_contact_institute = University Hospital Friedrich Alexander Universitaet Erlangen-Nuernberg
!Sample_contact_address = Schwabachanlage 10
!Sample_contact_city = Erlangen
!Sample_contact_zip/postal_code = 91054
!Sample_contact_country = Germany
!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/SAMN15416974
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8647109
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4648nnn/GSM4648437/suppl/GSM4648437_Lung_OVA+SIA_Seurat_count_matrix.txt.gz
!Sample_series_id = GSE153632
!Sample_data_row_count = 0
^SAMPLE = GSM4648438
!Sample_title = Synovium_OVA+SIA
!Sample_geo_accession = GSM4648438
!Sample_status = Public on Nov 12 2020
!Sample_submission_date = Jul 01 2020
!Sample_last_update_date = Nov 12 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Synovial eosinophil granulocytes
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Hind paw synovial tissue
!Sample_characteristics_ch1 = strain: Balb/c
!Sample_characteristics_ch1 = cell type: CD45+CD11b+Siglec-F+ granulocytes
!Sample_characteristics_ch1 = treatment: OVA+SIA
!Sample_characteristics_ch1 = time point: Day 7 post SIA
!Sample_treatment_protocol_ch1 = To trigger eosinophilic asthma, 6 weeks old Balb/c mice were sensitized twice with intraperitoneal injection of 100µg OVA/Alum mixture at day -20 and -13, and challenged three times with intranasal injection of 50µg OVA at day -2, -1 and 0. At day 0, mice were injected with 150µl K/BxN serum intraperitoneally for inducing SIA. Mice were challenged again at day 4, 5, 6 with intranasal injection of 50µg OVA and sacrificed at day 7.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The  lungs of 3 mice were pooled for the sample Lung_OVA+SIA, 16 hind ankle joints (8 mice) were pooled for the sample Synovium_OVA+SIA and 24 hind ankle joints (12 mice) were pooled for the sample Synovium_SIA. Eosinophils were sorted via the markers CD45+ CD11b+ Siglec-F+. For each sample 8000 cells were loaded onto a Chromium Single Cell A Chip (10x Genomics) with Chromium Single Cell 3' v3 Gel Beads (10x Genomics) to generate single cell bead emulsions for reverse transcription and cell bar coding according to the manufacturers instructions
!Sample_extract_protocol_ch1 = Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v3 and i7 Mutiplex kit (10X Genomics) according to the manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2500 using the recommended read lengths for Chromium Single Cell 3' v3 chemistry.
!Sample_data_processing = Illumina RTA 1.18.66.3 was used for base calling
!Sample_data_processing = Base calling files were converted to FASTQ files and demultiplexed using Cell Ranger v3.0.1 (10x Genomics) mkfastq with standard parameters.
!Sample_data_processing = Cell Ranger v3.0.1 quant was used to map the demultiplexed reads to the reference genome (mm10, v3.0.0, 10x Genomics), process cell barcodes, generate expression matrices of UMI (unique molecule identifier) counts per droplet and estimate the number of cells using standard parameters.
!Sample_data_processing = Seurat v3.1.0 was used under R v3.6.1 to first remove low quality cells expressing less than 300 genes or more than 20% mitochondrial genes or both. The filtered cells were clustered by similarity in gene expression and visualized. For the clusters marker genes were determined.
!Sample_data_processing = To compare between tissues, data sets were integrated follwing the recommended approach for SCT-transformed data in Seurat v3.1.0
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: tab delimited text files with UMI counts per gene per cell after filtering in Seurat (min.cells = 3, min.genes = 300)
!Sample_platform_id = GPL17021
!Sample_contact_name = Philipp,,Kirchner
!Sample_contact_department = Institute of Human Genetics
!Sample_contact_institute = University Hospital Friedrich Alexander Universitaet Erlangen-Nuernberg
!Sample_contact_address = Schwabachanlage 10
!Sample_contact_city = Erlangen
!Sample_contact_zip/postal_code = 91054
!Sample_contact_country = Germany
!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/SAMN15416973
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8647110
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4648nnn/GSM4648438/suppl/GSM4648438_Synovium_OVA+SIA_Seurat_count_matrix.txt.gz
!Sample_series_id = GSE153632
!Sample_data_row_count = 0
^SAMPLE = GSM4648439
!Sample_title = Synovium_SIA
!Sample_geo_accession = GSM4648439
!Sample_status = Public on Nov 12 2020
!Sample_submission_date = Jul 01 2020
!Sample_last_update_date = Nov 12 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Synovial eosinophil granulocytes
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Hind paw synovial tissue
!Sample_characteristics_ch1 = strain: Balb/c
!Sample_characteristics_ch1 = cell type: CD45+CD11b+Siglec-F+ granulocytes
!Sample_characteristics_ch1 = treatment: SIA
!Sample_characteristics_ch1 = time point: Day 7 post SIA
!Sample_treatment_protocol_ch1 = To trigger eosinophilic asthma, 6 weeks old Balb/c mice were sensitized twice with intraperitoneal injection of 100µg OVA/Alum mixture at day -20 and -13, and challenged three times with intranasal injection of 50µg OVA at day -2, -1 and 0. At day 0, mice were injected with 150µl K/BxN serum intraperitoneally for inducing SIA. Mice were challenged again at day 4, 5, 6 with intranasal injection of 50µg OVA and sacrificed at day 7.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The  lungs of 3 mice were pooled for the sample Lung_OVA+SIA, 16 hind ankle joints (8 mice) were pooled for the sample Synovium_OVA+SIA and 24 hind ankle joints (12 mice) were pooled for the sample Synovium_SIA. Eosinophils were sorted via the markers CD45+ CD11b+ Siglec-F+. For each sample 8000 cells were loaded onto a Chromium Single Cell A Chip (10x Genomics) with Chromium Single Cell 3' v3 Gel Beads (10x Genomics) to generate single cell bead emulsions for reverse transcription and cell bar coding according to the manufacturers instructions
!Sample_extract_protocol_ch1 = Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v3 and i7 Mutiplex kit (10X Genomics) according to the manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2500 using the recommended read lengths for Chromium Single Cell 3' v3 chemistry.
!Sample_data_processing = Illumina RTA 1.18.66.3 was used for base calling
!Sample_data_processing = Base calling files were converted to FASTQ files and demultiplexed using Cell Ranger v3.0.1 (10x Genomics) mkfastq with standard parameters.
!Sample_data_processing = Cell Ranger v3.0.1 quant was used to map the demultiplexed reads to the reference genome (mm10, v3.0.0, 10x Genomics), process cell barcodes, generate expression matrices of UMI (unique molecule identifier) counts per droplet and estimate the number of cells using standard parameters.
!Sample_data_processing = Seurat v3.1.0 was used under R v3.6.1 to first remove low quality cells expressing less than 300 genes or more than 20% mitochondrial genes or both. The filtered cells were clustered by similarity in gene expression and visualized. For the clusters marker genes were determined.
!Sample_data_processing = To compare between tissues, data sets were integrated follwing the recommended approach for SCT-transformed data in Seurat v3.1.0
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: tab delimited text files with UMI counts per gene per cell after filtering in Seurat (min.cells = 3, min.genes = 300)
!Sample_platform_id = GPL17021
!Sample_contact_name = Philipp,,Kirchner
!Sample_contact_department = Institute of Human Genetics
!Sample_contact_institute = University Hospital Friedrich Alexander Universitaet Erlangen-Nuernberg
!Sample_contact_address = Schwabachanlage 10
!Sample_contact_city = Erlangen
!Sample_contact_zip/postal_code = 91054
!Sample_contact_country = Germany
!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/SAMN15416972
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8647111
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4648nnn/GSM4648439/suppl/GSM4648439_Synovium_SIA_Seurat_count_matrix.txt.gz
!Sample_series_id = GSE153632
!Sample_data_row_count = 0