|
| Status |
Public on Nov 14, 2012 |
| Title |
BRD4_untreated_Tcell_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4+ T cells
chip antibody: BRD4 (Abcam; Cat no. ab46199; Lot no. 613288)
treatment: untreated
|
| Treatment protocol |
Freshly isolated human CD4+ T-cells treated with or without 500nM JQ1 for 24hr
|
| Growth protocol |
CD4+ T-cells were purified from normal human peripheral blood using the human CD4+ T-cell Isolation Kit II (Miltenyl Biotech).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP DNA ends were repaired using PNK and Klenow enzyme followed by treatment with Taq polymerase to generate an overhanging 3’ adenine base for adaptor ligation. The repaired ends were then ligated to a pair of Solexa adaptors and ChIP DNA was amplified for 17 cycles using adaptor primers. The amplified DNA was separated using an agarose gel and DNA fragments around 220bp were isolated and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using ELAND of the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.01 using the landerwaterman algorithm.
Normalization (wig normalized files): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)
|
| |
|
| Submission date |
Oct 27, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Keh-chuang Chin |
| E-mail(s) |
kehchuang_chin@immunol.a-star.edu.sg
|
| Organization name |
Singapore Immunology Network
|
| Department |
Laboratory of Gene Regulation
|
| Street address |
Biopolis, 8A Biomedical Grove, #03-06 Immunos
|
| City |
Singapore |
| ZIP/Postal code |
138648 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE33281 |
Bromodomain-Containing-Protein 4 (BRD4) Regulates RNA Polymerase II Serine 2 Phosphorylation in Human CD4+ T Cells |
|
| Relations |
| SRA |
SRX103444 |
| BioSample |
SAMN00744451 |
