|
| Status |
Public on Nov 21, 2014 |
| Title |
Pol_II ChIP-seq_kelly_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
high-MYCN-Neuroblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Neuroblastoma cell line
cell line: kelly
passages: 5 to 12
chip antibody: Pol_II (SantaCruz sc-899)
|
| Treatment protocol |
100 nM THZ1 or DMSO for 3hrs.
|
| Growth protocol |
RPMI 1640 + FBS.
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
For all samples reads were aligned to their indicated build using bowtie with parameters -t -v 2 -m --strata --best.
ChIP-seq peaks were detected using MACS (version 1.4.2) The default p-value threshold of enrichment of 1 x 10−5 was used for all data sets. we ran MACS three times with the options --keep-dup=none, --keep-dup=1, and --keep-dup=all
For each cell type, the three sets of MACS peaks were merged using BEDTools (Quinlan and Hall, 2010). In all cases we used the additional MACS parameter -m 10,500.
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: peak positions
|
| |
|
| Submission date |
Oct 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Rani George |
| E-mail(s) |
[email protected]
|
| Phone |
617-632-5281
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Rani George Lab
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE62725 |
Targeting of Super-Enhancer-Associated Oncogenic Transcription in MYCN-driven tumor cells by CDK7 inhibition [ChIP-Seq] |
| GSE62726 |
Targeting of Super-Enhancer-Associated Oncogenic Transcription in MYCN-driven tumor cells by CDK7 inhibition |
|
| Relations |
| BioSample |
SAMN03144692 |
| SRA |
SRX743832 |
