|
| Status |
Public on Oct 20, 2015 |
| Title |
mutHEK293_CTCF |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Kidney (HEK)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293T
chip antibody: CTCF
antibody manu.: Millipore
antibody catalog: 07-729
young_id: 20150925_4264
|
| Growth protocol |
H293T cells were cultured in DMEM + 10% serum at 37°C / 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
sonication
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
|
| |
|
| Submission date |
Oct 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE68976 |
Activation of proto-oncogenes by disruption of chromosome neighborhoods [ChIP-Seq] |
| GSE68978 |
Activation of proto-oncogenes by disruption of chromosome neighborhoods |
|
| Relations |
| BioSample |
SAMN04194065 |
| SRA |
SRX1353402 |
