|
| Status |
Public on Nov 09, 2021 |
| Title |
Kelly_JQAD_6h_H3K27ac_r1 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: JQAD 6h
cell line: Kelly
cell type: Neuroblastoma
chip antibody: H3K27ac
antibody manu.: Abcam
antibody catalog: ab4729
antibody lot: GR3231887-1
|
| 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 |
Reads were aligned to the dm6 reference genome using bowtie -k 1 --best. Non-mapping reads were aligned to the hg19 reference genome using bowtie -k 2 -m 2 --best -l 75 --chunkmbs 256
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 normalized to millions of reads mapped to the fly genome
|
| |
|
| 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) |
| GSE159614 |
EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma [ChIP-rx] |
| GSE159617 |
EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma |
|
| Relations |
| BioSample |
SAMN16477008 |
| SRA |
SRX9309672 |
