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Sample GSM6357589 Query DataSets for GSM6357589
Status Public on Feb 02, 2024
Title Liver Tconv cells, CCl4, sample 5
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics tissue: liver
cell type: Liver Tconv cells
strain: C57BL/6
Sex: male
genotype: Foxp3GFP
treatment: CCl4
Treatment protocol CD4+ Treg and Tconv cells were FACS purified from livers and spleens of male Foxp3GFP mice, either control, CCl4 treated, or fed the CDAA-HFD diet.
Extracted molecule total RNA
Extraction protocol Cells were FACS-sorted into Trizol Reagent, and RNA was extracted using a Qiagen kit
Clontech Ultra Low v4 kit for cDNA synthesis followed by NexteraXT
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Liver_Tconv_CCl4_5
Data processing Libraries were then sequenced using Illumina NovaSeq 6000, with multiplexed samples in each lane, which yields targeted number of paired-end 100bp reads for each sample
RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Mouse:GRCm38.p6) using kallisto (0.44.0).
Differentially expressed genes were assessed through DESeq2
Assembly: Ensembl v96, Mouse:GRCm38.p6
Supplementary files format and content: .tsv, abundance output from Kallisto that includes estimated counts, TPM, effective length for each transcript.
Submission date Jul 20, 2022
Last update date Feb 02, 2024
Contact name Nicholas Arpaia
Organization name Columbia University
Department Microbiology & Immunology
Street address 701 West 168th Street
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platform ID GPL24247
Series (2)
GSE208641 Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis I
GSE208706 Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis
BioSample SAMN29844758
SRA SRX16358861

Supplementary file Size Download File type/resource
GSM6357589_TN028.tsv.gz 1.6 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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