|
| Status |
Public on Oct 21, 2014 |
| Title |
Total T IgG |
| Sample type |
SRA |
| |
|
| Source name |
T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: T cells
tissue: Spleen
chip antibody: Rabbit IgG (R&D systems.)
|
| Treatment protocol |
For ChIP-Seq,Total T cells were stimulated with TCR for indicated time.
|
| Growth protocol |
Naïve CD4+ T cells from spleen and lymph nodes were purified from 6 week old mice using a CD4+CD62+ T cell Isolation Kit II (Miltenyi). Cells were activated with 2 μg/ml plate-bound anti-CD3 + 1 μg/ml soluble anti-CD28 (PharMingen)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-Seq, chromatin was prepared from cells cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication and the ChIP DNA was blunt-ended, ligated to the Solexa adaptor and amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP against IgG
|
| Data processing |
For ChIP-Seq and RNA-Seq, Basecalls performed using CASAVA 1.8 (HiSeq2000)
Raw reads were aligned to the mm9 mouse genome assembly using Bowtie 0.12.7
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts
For ChIP-Seq, peaks are called using MACS 1.3.7.1
Genome_build: mm9
Supplementary_files_format_and_content: BED files are generated using BEDTOOLS and unpublished python scripts, rpkm (abundance measurement) files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts
|
| |
|
| Submission date |
Jul 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Peng Li |
| E-mail(s) |
[email protected]
|
| Organization name |
NIH
|
| Department |
NHLBI
|
| Lab |
LMI
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE49366 |
EGR2 is Critical for Peripheral Naïve T Cell Differentiation and the T-cell Response to Influenza |
|
| Relations |
| BioSample |
SAMN02297739 |
| SRA |
SRX329254 |
