|
Status |
Public on Feb 02, 2024 |
Title |
Treg, spleen_GEX |
Sample type |
SRA |
|
|
Source name |
spleen
|
Organism |
Mus musculus |
Characteristics |
tissue: spleen cell type: Treg cells strain: C57BL/6 Sex: male genotype: Foxp3GFP treatment: multiplexed sample: control and NASH
|
Treatment protocol |
Single cell RNA-seq (cell hashing and TCRseq) of Treg cells enriched via FACS from the liver, spleen and visceral adipose tissue from Foxp3GFP mice fed normal chow or a NASH diet.
|
Extracted molecule |
total RNA |
Extraction protocol |
Viable CD4+GFP+ cells were sorted using a FACS Aria cell sorter 10x Genomics Single Cell 5’ workflow for gene expression, cell hashing, and full-length V(D)J T cell receptor sequencing
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
Hashtag 1-3 are normal diet and Hashtag 4-7 are NASH. NT016
|
Data processing |
Libraries were then sequenced on an Illumina NovaSeq 6000 CellRanger 6.1.2 was used to process the sequencing data Analysis was subsequently performed using Seurat 4.2.0 Supplementary files format and content: tar file containing processed CellRanger output for barcodes, features, matrix
|
|
|
Submission date |
Jun 06, 2023 |
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) |
GSE208706 |
Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis |
GSE234244 |
Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis [scTreg] |
|
Relations |
BioSample |
SAMN35640765 |
SRA |
SRX20601688 |