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Sample GSM6357586 Query DataSets for GSM6357586
Status Public on Feb 02, 2024
Title Liver Tconv cells, CCl4, sample 3
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_3
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
E-mail(s) na2697@cumc.columbia.edu
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
Relations
BioSample SAMN29844760
SRA SRX16358859

Supplementary file Size Download File type/resource
GSM6357586_TN026.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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