|
| Status |
Public on Feb 23, 2017 |
| Title |
HeLa.ENL_Flag |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: control
chip antibody: Sigma F1804
|
| Treatment protocol |
For Flag-tagged stable cell selection, 10 ug/ml blasticidin was used for stable cells selection. For iCas9 induced ENL CRISPR knockout, 1ug/ml of doxycycline was used for induction of 5days before collecting for ChIP.
|
| Growth protocol |
Cells were maintained in DMEM with 10% FBS, 5% CO2, 37oC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
Sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6+B102; Scores represent the ChIP-seq tag numbers
|
| |
|
| Submission date |
Oct 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hong Wen |
| Organization name |
Van Andel Research Institute
|
| Department |
Center for Epigenetics
|
| Street address |
333 Bostwick Ave. N.E.
|
| City |
Grand Rapids |
| State/province |
Michigan |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE80779 |
ENL Links Histone Acetylation to Oncogenic Gene Expression in AML |
|
| Relations |
| SRA |
SRX2266662 |
| BioSample |
SAMN05935477 |
