|
| Status |
Public on Mar 25, 2024 |
| Title |
IpH3K27AcChPSeq-HAP1-siMZ-lib6-4122021_S23_L003 |
| Sample type |
SRA |
| |
|
| Source name |
HAP1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HAP1
cell type: HAP1-MAZKO
chip antibody: ab4729
|
| Growth protocol |
HAP1 control cells and MAZ KO cells are cultured in IMDM with 10% FBS and 1% Pen/Strep. K562 control cells and MAZ knocking down cells were grown in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, 10 mM HEPES (pH 7.3), and 1% penicillin-streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) was performed with a ChIP-IT Express kit following manufacturer's instructions.
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor plus (Diagenode).
ChIP-Seq libraries were prepared using the “NEBNext® Ultra™ II DNA Library Prep Kit”. Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2. Peaks were called using MACS2. Bigwig files were generated with Deeptools.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
|
| |
|
| Submission date |
Oct 08, 2022 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Gary Felsenfeld |
| E-mail(s) |
txiao2015@gmail.com
|
| Organization name |
NIH
|
| Lab |
LMB
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE215081 |
The Myc-Associated Zinc Finger Protein (MAZ) controls STAT1-mediated antiviral response by reshaping epigenome [ChIP-Seq] |
| GSE215083 |
The Myc-Associated Zinc Finger Protein (MAZ) controls STAT1-mediated antiviral response by reshaping epigenome |
|
| Relations |
| BioSample |
SAMN31215646 |
| SRA |
SRX17833899 |
