|
| Status |
Public on Aug 15, 2017 |
| Title |
CD4+ Th1 Low IL-2 + aKG CTCF Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ Th1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: CD4+ Th1
antibody: CTCF
|
| Growth protocol |
Primary CD4+ T cells were isolated from spleen and lymph nodes of C57BL/6 mice and stimulated with plate bound anti-CD3 and anti-CD28 in type 1 conditions (IL-12 and anti-IL4). On day 3, the cells were split and maintained in either high IL-2, low IL-2, or low IL-2 with αKG. The low IL-2 and low IL-2 with aKG replicate 1 for H3K27Ac and H3K27me3 were performed with 10 units/mL of IL-2. All other replicates were performed as described in Chisolm et. al.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq assays were performed as previously outlined (Reddy et al. Genome Research 2009, PMID: 19801529)
Library construction was performed as previously outlined (Reddy et al. Genome Research 2009, PMID: 19801529)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SL136332
|
| Data processing |
Reads were aligned to the mm9 genome using Bowtie to generate BAM files
Bedgraph files were generated from BAM files using Bedtools
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph
|
| |
|
| Submission date |
Nov 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Amy Weinmann |
| Organization name |
University of Alabama at Birmingham
|
| Department |
Department of Microbiology
|
| Street address |
1825 University Blvd
|
| City |
Birmingham |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE88857 |
CTCF translates IL-2- and αKG-sensitive metabolic changes in T cells into context-dependent differentiation gene programs [ChIP-Seq] |
| GSE89722 |
CTCF translates IL-2- and aKG-sensitive metabolic changes in T cells into context-dependent differentiation gene programs |
|
| Relations |
| BioSample |
SAMN06014531 |
| SRA |
SRX2345176 |
