|
| Status |
Public on Jun 04, 2013 |
| Title |
MelJuSo etoposide H3K4me3 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
MelJuSo cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human skin melanoma cell line
treatment: Etoposide 60uM 2 hours
time point: 24 hours post drug removal
cell line: MelJuSo
chip antibody: H3K4me3
chip antibody manufacturer: Abcam
chip antibody catalog #: ab1012
chip antibody lot #: 814968
|
| Treatment protocol |
Cells were treated with indicated drugs for 2 hours and followed by extensive washing . Cells were further cultured for another 24 hours before cells were fixed and subjected for ChIP procedures.
|
| Growth protocol |
Cells were grown in 15cm dishes around 80% confluency.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After fixation, lysates were cleared from sonicated nuclei and antibodies against H3K4me3 were used to IP the histone-DNA complexes. Libraries were prepared according to the provider’s kits and protocols for ChIP samples.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against H3K4me3
|
| Data processing |
Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 60 were removed.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm with default parameter.
|
| |
|
| Submission date |
Nov 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Baoxu Pang |
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Michael Snyder
|
| Street address |
3165 Porter Drive
|
| City |
Palo Alto |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE33633 |
Epigenetic changes due to histone eviction induced by anthracycline doxorubicin and aclarubicin |
| GSE33634 |
Topoisomerase II inhibitors and histone eviction |
|
| Relations |
| SRA |
SRX105599 |
| BioSample |
SAMN00754064 |
