|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 02, 2024 |
Title |
Liver Treg cells, CCl4, sample 1 |
Sample type |
SRA |
|
|
Source name |
liver
|
Organism |
Mus musculus |
Characteristics |
tissue: liver cell type: Liver Treg 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_Treg_CCl4_1
|
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 |
SAMN29844770 |
SRA |
SRX16358849 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6357572_TN016.tsv.gz |
1.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|