^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 = GSE167540
!Series_title = The IL-33 receptor ST2 is expressed on IL-4+ and IL-13+ human tissue eosinophils in eosinophilic esophagitis
!Series_geo_accession = GSE167540
!Series_status = Public on Feb 01 2022
!Series_submission_date = Feb 25 2021
!Series_last_update_date = May 03 2022
!Series_pubmed_id = 34614218
!Series_summary = Eosinophilic esophagitis (EoE) is a chronic type 2 allergic disease of the esophagus characterized by eosinophil mucosal infiltration. The role of the allergic cytokine IL-33 and its receptor ST2 in EoE is poorly understood. We employed single cell RNA sequencing on human blood eosinophils and esophageal biopsies from EoE patients. Our goal was to characterize an eosinophil transcriptional signature and identify the transcriptional and cellular landscape in the EoE esophagus as well as targets and downstream effects of IL-33 signaling in EoE.
!Series_overall_design = PBMCs and esophageal tissue were collected from 4 patients with EoE.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Amiko,M,Uchida
!Series_contributor = Patrick,J,Lenehan
!Series_contributor = Praveen,,Vimalathas
!Series_contributor = Kaia,C,Miller
!Series_contributor = Mabel,,Valencia-Yang
!Series_contributor = Li,,Qiang
!Series_contributor = Lauren,A,Canha
!Series_contributor = Lestat,R,Ali
!Series_contributor = Michael,,Dougan
!Series_contributor = John,J,Garber
!Series_contributor = Stephanie,K,Dougan
!Series_sample_id = GSM5106951
!Series_sample_id = GSM5106952
!Series_sample_id = GSM5106953
!Series_sample_id = GSM5106954
!Series_sample_id = GSM5106955
!Series_sample_id = GSM5106956
!Series_sample_id = GSM5106957
!Series_sample_id = GSM5106958
!Series_contact_name = Stephanie,,Dougan
!Series_contact_email = stephanie_dougan@dfci.harvard.edu
!Series_contact_department = Cancer Immunology & Virology
!Series_contact_institute = Dana-Farber Cancer Institute
!Series_contact_address = 1 Jimmy Fund Way
!Series_contact_city = Boston
!Series_contact_state = MA
!Series_contact_zip/postal_code = 02215
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE167nnn/GSE167540/suppl/GSE167540_RAW.tar
!Series_platform_id = GPL16791
!Series_platform_taxid = 9606
!Series_sample_taxid = 9606
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA704920
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP308215
^PLATFORM = GPL16791
!Platform_title = Illumina HiSeq 2500 (Homo sapiens)
!Platform_geo_accession = GPL16791
!Platform_status = Public on Mar 14 2013
!Platform_submission_date = Mar 14 2013
!Platform_last_update_date = Mar 27 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Homo sapiens
!Platform_taxid = 9606
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM5106951
!Sample_title = P1 Tissue scRNA-seq
!Sample_geo_accession = GSM5106951
!Sample_status = Public on Feb 01 2022
!Sample_submission_date = Feb 25 2021
!Sample_last_update_date = Feb 01 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Eosphageal tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = patient: P1
!Sample_characteristics_ch1 = disease state: Eosinophilic esophagitis (EoE)
!Sample_characteristics_ch1 = tissue: Eosphagus
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Whole blood underwent a Ficoll-Paque gradient, and fluorescence activated cell sorting on BD FACS Aria II was performed isolating live SSC-high, CD45+, CD16/CD203c- and CCR3+ cells.
!Sample_extract_protocol_ch1 = About 3000 cells per sample were encapsulated using the InDrops protocol.
!Sample_data_processing = Reads were aligned using bcbio-nextgen's single cell analysis pipeline.
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Gene-level counts are provided in Matrix Market formatted files for each sample separately.
!Sample_platform_id = GPL16791
!Sample_contact_name = Stephanie,,Dougan
!Sample_contact_email = stephanie_dougan@dfci.harvard.edu
!Sample_contact_department = Cancer Immunology & Virology
!Sample_contact_institute = Dana-Farber Cancer Institute
!Sample_contact_address = 1 Jimmy Fund Way
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02215
!Sample_contact_country = USA
!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/SAMN18057720
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10169502
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5106nnn/GSM5106951/suppl/GSM5106951_P1t.tar.gz
!Sample_series_id = GSE167540
!Sample_data_row_count = 0
^SAMPLE = GSM5106952
!Sample_title = P1 Blood scRNA-seq
!Sample_geo_accession = GSM5106952
!Sample_status = Public on Feb 01 2022
!Sample_submission_date = Feb 25 2021
!Sample_last_update_date = Feb 01 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = patient: P1
!Sample_characteristics_ch1 = disease state: Eosinophilic esophagitis (EoE)
!Sample_characteristics_ch1 = tissue: PBMC
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Whole blood underwent a Ficoll-Paque gradient, and fluorescence activated cell sorting on BD FACS Aria II was performed isolating live SSC-high, CD45+, CD16/CD203c- and CCR3+ cells.
!Sample_extract_protocol_ch1 = About 3000 cells per sample were encapsulated using the InDrops protocol.
!Sample_data_processing = Reads were aligned using bcbio-nextgen's single cell analysis pipeline.
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Gene-level counts are provided in Matrix Market formatted files for each sample separately.
!Sample_platform_id = GPL16791
!Sample_contact_name = Stephanie,,Dougan
!Sample_contact_email = stephanie_dougan@dfci.harvard.edu
!Sample_contact_department = Cancer Immunology & Virology
!Sample_contact_institute = Dana-Farber Cancer Institute
!Sample_contact_address = 1 Jimmy Fund Way
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02215
!Sample_contact_country = USA
!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/SAMN18057719
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10169503
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5106nnn/GSM5106952/suppl/GSM5106952_P1b.tar.gz
!Sample_series_id = GSE167540
!Sample_data_row_count = 0
^SAMPLE = GSM5106953
!Sample_title = P2 Tissue scRNA-seq
!Sample_geo_accession = GSM5106953
!Sample_status = Public on Feb 01 2022
!Sample_submission_date = Feb 25 2021
!Sample_last_update_date = Feb 01 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Eosphageal tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = patient: P2
!Sample_characteristics_ch1 = disease state: Eosinophilic esophagitis (EoE)
!Sample_characteristics_ch1 = tissue: Eosphagus
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Whole blood underwent a Ficoll-Paque gradient, and fluorescence activated cell sorting on BD FACS Aria II was performed isolating live SSC-high, CD45+, CD16/CD203c- and CCR3+ cells.
!Sample_extract_protocol_ch1 = About 3000 cells per sample were encapsulated using the InDrops protocol.
!Sample_data_processing = Reads were aligned using bcbio-nextgen's single cell analysis pipeline.
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Gene-level counts are provided in Matrix Market formatted files for each sample separately.
!Sample_platform_id = GPL16791
!Sample_contact_name = Stephanie,,Dougan
!Sample_contact_email = stephanie_dougan@dfci.harvard.edu
!Sample_contact_department = Cancer Immunology & Virology
!Sample_contact_institute = Dana-Farber Cancer Institute
!Sample_contact_address = 1 Jimmy Fund Way
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02215
!Sample_contact_country = USA
!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/SAMN18057718
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10169504
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5106nnn/GSM5106953/suppl/GSM5106953_P2t.tar.gz
!Sample_series_id = GSE167540
!Sample_data_row_count = 0
^SAMPLE = GSM5106954
!Sample_title = P2 Blood scRNA-seq
!Sample_geo_accession = GSM5106954
!Sample_status = Public on Feb 01 2022
!Sample_submission_date = Feb 25 2021
!Sample_last_update_date = Feb 01 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = patient: P2
!Sample_characteristics_ch1 = disease state: Eosinophilic esophagitis (EoE)
!Sample_characteristics_ch1 = tissue: PBMC
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Whole blood underwent a Ficoll-Paque gradient, and fluorescence activated cell sorting on BD FACS Aria II was performed isolating live SSC-high, CD45+, CD16/CD203c- and CCR3+ cells.
!Sample_extract_protocol_ch1 = About 3000 cells per sample were encapsulated using the InDrops protocol.
!Sample_data_processing = Reads were aligned using bcbio-nextgen's single cell analysis pipeline.
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Gene-level counts are provided in Matrix Market formatted files for each sample separately.
!Sample_platform_id = GPL16791
!Sample_contact_name = Stephanie,,Dougan
!Sample_contact_email = stephanie_dougan@dfci.harvard.edu
!Sample_contact_department = Cancer Immunology & Virology
!Sample_contact_institute = Dana-Farber Cancer Institute
!Sample_contact_address = 1 Jimmy Fund Way
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02215
!Sample_contact_country = USA
!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/SAMN18057717
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10169505
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5106nnn/GSM5106954/suppl/GSM5106954_P2b.tar.gz
!Sample_series_id = GSE167540
!Sample_data_row_count = 0
^SAMPLE = GSM5106955
!Sample_title = P3 Tissue scRNA-seq
!Sample_geo_accession = GSM5106955
!Sample_status = Public on Feb 01 2022
!Sample_submission_date = Feb 25 2021
!Sample_last_update_date = Feb 01 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Eosphageal tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = patient: P3
!Sample_characteristics_ch1 = disease state: Eosinophilic esophagitis (EoE)
!Sample_characteristics_ch1 = tissue: Eosphagus
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Whole blood underwent a Ficoll-Paque gradient, and fluorescence activated cell sorting on BD FACS Aria II was performed isolating live SSC-high, CD45+, CD16/CD203c- and CCR3+ cells.
!Sample_extract_protocol_ch1 = About 3000 cells per sample were encapsulated using the InDrops protocol.
!Sample_data_processing = Reads were aligned using bcbio-nextgen's single cell analysis pipeline.
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Gene-level counts are provided in Matrix Market formatted files for each sample separately.
!Sample_platform_id = GPL16791
!Sample_contact_name = Stephanie,,Dougan
!Sample_contact_email = stephanie_dougan@dfci.harvard.edu
!Sample_contact_department = Cancer Immunology & Virology
!Sample_contact_institute = Dana-Farber Cancer Institute
!Sample_contact_address = 1 Jimmy Fund Way
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02215
!Sample_contact_country = USA
!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/SAMN18057716
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10169506
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5106nnn/GSM5106955/suppl/GSM5106955_P3t.tar.gz
!Sample_series_id = GSE167540
!Sample_data_row_count = 0
^SAMPLE = GSM5106956
!Sample_title = P3 Blood scRNA-seq
!Sample_geo_accession = GSM5106956
!Sample_status = Public on Feb 01 2022
!Sample_submission_date = Feb 25 2021
!Sample_last_update_date = Feb 01 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = patient: P3
!Sample_characteristics_ch1 = disease state: Eosinophilic esophagitis (EoE)
!Sample_characteristics_ch1 = tissue: PBMC
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Whole blood underwent a Ficoll-Paque gradient, and fluorescence activated cell sorting on BD FACS Aria II was performed isolating live SSC-high, CD45+, CD16/CD203c- and CCR3+ cells.
!Sample_extract_protocol_ch1 = About 3000 cells per sample were encapsulated using the InDrops protocol.
!Sample_data_processing = Reads were aligned using bcbio-nextgen's single cell analysis pipeline.
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Gene-level counts are provided in Matrix Market formatted files for each sample separately.
!Sample_platform_id = GPL16791
!Sample_contact_name = Stephanie,,Dougan
!Sample_contact_email = stephanie_dougan@dfci.harvard.edu
!Sample_contact_department = Cancer Immunology & Virology
!Sample_contact_institute = Dana-Farber Cancer Institute
!Sample_contact_address = 1 Jimmy Fund Way
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02215
!Sample_contact_country = USA
!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/SAMN18057715
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10169507
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5106nnn/GSM5106956/suppl/GSM5106956_P3b.tar.gz
!Sample_series_id = GSE167540
!Sample_data_row_count = 0
^SAMPLE = GSM5106957
!Sample_title = P4 Tissue scRNA-seq
!Sample_geo_accession = GSM5106957
!Sample_status = Public on Feb 01 2022
!Sample_submission_date = Feb 25 2021
!Sample_last_update_date = Feb 01 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Eosphageal tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = patient: P4
!Sample_characteristics_ch1 = disease state: Eosinophilic esophagitis (EoE)
!Sample_characteristics_ch1 = tissue: Eosphagus
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Whole blood underwent a Ficoll-Paque gradient, and fluorescence activated cell sorting on BD FACS Aria II was performed isolating live SSC-high, CD45+, CD16/CD203c- and CCR3+ cells.
!Sample_extract_protocol_ch1 = About 3000 cells per sample were encapsulated using the InDrops protocol.
!Sample_data_processing = Reads were aligned using bcbio-nextgen's single cell analysis pipeline.
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Gene-level counts are provided in Matrix Market formatted files for each sample separately.
!Sample_platform_id = GPL16791
!Sample_contact_name = Stephanie,,Dougan
!Sample_contact_email = stephanie_dougan@dfci.harvard.edu
!Sample_contact_department = Cancer Immunology & Virology
!Sample_contact_institute = Dana-Farber Cancer Institute
!Sample_contact_address = 1 Jimmy Fund Way
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02215
!Sample_contact_country = USA
!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/SAMN18057714
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10169508
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5106nnn/GSM5106957/suppl/GSM5106957_P4t.tar.gz
!Sample_series_id = GSE167540
!Sample_data_row_count = 0
^SAMPLE = GSM5106958
!Sample_title = P4 Blood scRNA-seq
!Sample_geo_accession = GSM5106958
!Sample_status = Public on Feb 01 2022
!Sample_submission_date = Feb 25 2021
!Sample_last_update_date = Feb 01 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = patient: P4
!Sample_characteristics_ch1 = disease state: Eosinophilic esophagitis (EoE)
!Sample_characteristics_ch1 = tissue: PBMC
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Whole blood underwent a Ficoll-Paque gradient, and fluorescence activated cell sorting on BD FACS Aria II was performed isolating live SSC-high, CD45+, CD16/CD203c- and CCR3+ cells.
!Sample_extract_protocol_ch1 = About 3000 cells per sample were encapsulated using the InDrops protocol.
!Sample_data_processing = Reads were aligned using bcbio-nextgen's single cell analysis pipeline.
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Gene-level counts are provided in Matrix Market formatted files for each sample separately.
!Sample_platform_id = GPL16791
!Sample_contact_name = Stephanie,,Dougan
!Sample_contact_email = stephanie_dougan@dfci.harvard.edu
!Sample_contact_department = Cancer Immunology & Virology
!Sample_contact_institute = Dana-Farber Cancer Institute
!Sample_contact_address = 1 Jimmy Fund Way
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02215
!Sample_contact_country = USA
!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/SAMN18057713
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10169509
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5106nnn/GSM5106958/suppl/GSM5106958_P4b.tar.gz
!Sample_series_id = GSE167540
!Sample_data_row_count = 0