^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 = GSE162651
!Series_title = Dynamic Shifts in the Composition of Resident and Recruited Macrophages Influence Tissue Remodeling in NASH
!Series_geo_accession = GSE162651
!Series_status = Public on Dec 31 2020
!Series_submission_date = Dec 04 2020
!Series_last_update_date = Jan 02 2021
!Series_summary = NASH is associated with signficant changes in liver macrophage composition.  To gain insight into this heterogenity we performed scRNA on liver myeloid cells from mice fed a HFD for 16 weeks.
!Series_overall_design = Three C57CL/6 male mice were fed High fat, high sucrose diet (Research Diets -cat# D12492) for 16 weeks after which immune cells were isolated from the liver using portal vein perfusion and a percoll gradient protocol. The cells underwent flow sorting on live singlet cells and were gated on CD11bhi, F4/80int and CD11bint, F4/80hi populations.  Eosinophils and neutrophils were removed using Ly6G and siglecF exlusion. Samples of these macrophages were mixed 1:1 and the 3 mouse samples were pooled to create a signal sample for scRNA seq.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Sabine,,Daemen
!Series_contributor = Anastasiia,,Gainullina
!Series_contributor = Gowri,,Kalugotla
!Series_contributor = Li,,He
!Series_contributor = Mandy,M,Chan
!Series_contributor = Joseph,W,Beals
!Series_contributor = Kim,H,Liss
!Series_contributor = Samuel,,Klein
!Series_contributor = Ariel,E,Feldstein
!Series_contributor = Maxim,N,Artyomov
!Series_contributor = Brian,N,Finck
!Series_contributor = Joel,D,Schilling
!Series_sample_id = GSM4956216
!Series_contact_name = Maxim,N.,Artyomov
!Series_contact_email = martyomov@pathology.wustl.edu
!Series_contact_department = Immunology&Pathology
!Series_contact_institute = Washington University in St.Louis
!Series_contact_address = 660 S. Euclid Avenue, Campus Box 8118
!Series_contact_city = St.Louis
!Series_contact_state = MO
!Series_contact_zip/postal_code = 63110
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE162nnn/GSE162651/suppl/GSE162651_RAW.tar
!Series_platform_id = GPL24247
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682557
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP295857
^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 = GSM4956216
!Sample_title = Macrophages from a NASH liver, High_Fat diet
!Sample_geo_accession = GSM4956216
!Sample_status = Public on Dec 31 2020
!Sample_submission_date = Dec 04 2020
!Sample_last_update_date = Dec 31 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = macrophages from a NASH liver
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_characteristics_ch1 = tissue: NASH liver
!Sample_characteristics_ch1 = cell type: macrophages
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Cell-barcoded cDNA was generated from single cells via an oligo-dT priming approach. Single cells were captured into droplets utilizing the 10X Chromium system.  A sequencing library was generated from the 3' fragments containing the barcode.
!Sample_extract_protocol_ch1 = NovaSeq S4
!Sample_data_processing = quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
!Sample_data_processing = sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v3.0.2)
!Sample_data_processing = barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
!Sample_data_processing = single-cell 5′ gene counting , Cell Ranger Single Cell Software Suite (v3.0.2)
!Sample_data_processing = alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.
!Sample_platform_id = GPL24247
!Sample_contact_name = Maxim,N.,Artyomov
!Sample_contact_email = martyomov@pathology.wustl.edu
!Sample_contact_department = Immunology&Pathology
!Sample_contact_institute = Washington University in St.Louis
!Sample_contact_address = 660 S. Euclid Avenue, Campus Box 8118
!Sample_contact_city = St.Louis
!Sample_contact_state = MO
!Sample_contact_zip/postal_code = 63110
!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/SAMN16998632
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9631797
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4956nnn/GSM4956216/suppl/GSM4956216_High_Fat_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4956nnn/GSM4956216/suppl/GSM4956216_High_Fat_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4956nnn/GSM4956216/suppl/GSM4956216_High_Fat_matrix.mtx.gz
!Sample_series_id = GSE162651
!Sample_data_row_count = 0