|
| Status |
Public on Nov 09, 2021 |
| Title |
Kelly_EP300_MWZ5393 [Lab: Look] |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Kelly
cell type: Neuroblastoma
chip antibody: p300
antibody manu.: Abcam
antibody catalog: ab10485
antibody lot: GR215687-32
young_id: 20180324_7007
|
| Growth protocol |
Neuroblastoma cell lines were cultured in RPMI media containing 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin and validated to be free of Mycoplasma species by routine testing.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each ChIP, 10 μg of antibody was added to 3 ml of sonicated nuclear extract. Illumina sequencing, library construction and ChIP-seq analysis methods were previously described (Mansour et al. Science, 2014)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
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, 2020 |
| Last update date |
Nov 09, 2021 |
| Contact name |
Brian J Abraham |
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Computational Biology
|
| Street address |
262 Danny Thomas Blvd
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38112 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE159613 |
EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma [ChIP-seq] |
| GSE159617 |
EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma |
|
| Relations |
| BioSample |
SAMN16477009 |
| SRA |
SRX9309562 |
