|
| Status |
Public on Aug 04, 2016 |
| Title |
Foxp3_GFPKO_post_Tfx_rep2 (Sample 76) |
| Sample type |
SRA |
| |
|
| Source name |
Foxp3_GFPKO_post_Tfx
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen and peripheral lymph nodes
cell type: Inflammation-experienced cells expressing a Foxp3 reporter-null allele
source: Foxp3-GFPKO CD45.1
activating stimulus: Genetic Treg cell deficiency
days post-stimulus: NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted cells were lysed with TRIzol and stored at -80 degree. RNA was extracted according to the manufacturer’s manual (Life Technologies). cDNA libraries were generated using SMARTer amplification (Clontech) and individually indexed. Libraries were sequenced on HiSeq 2000 platform (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GFP+ CD45.1+ CD4 T cells were isolated from animals hemizigous for the Foxp3GFPKO allele. and transferred into Foxp3-GFP-DTR mice. Recipients underwent suboptimal Treg depletion prior to transfer to increase recovery of donor cells. GFP+CD45.1+ cells were isolated 1 month post-transfer for RNA-seq
|
| Data processing |
Sequences mapped using STAR 2.5.0
Expression level was quantified with refGene annotation
DESeq2 analysis was run with q-value cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: [htseq.txt and bam-genes.txt] DESeq2-normalized read counts for RNA-Seq samples
Supplementary_files_format_and_content: [countsatatacseqpeaks.txt] peaks for ATAC-Seq and ChIP-Seq samples
|
| |
|
| Submission date |
Jun 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hyein Sophia Cho |
| E-mail(s) |
[email protected]
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Developmental Biology
|
| Street address |
430 E 67th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE83315 |
Memory of inflammation in regulatory T cells |
|
| Relations |
| BioSample |
SAMN05240673 |
| SRA |
SRX1842303 |
