|
| Status |
Public on Mar 25, 2024 |
| Title |
Input-K562-Ctr-IFN |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cell line: K562
cell type: erythroleukemia
chip antibody: Inp
treatment: IFNg treated
|
| Treatment protocol |
HAP1 control cells and MAZ knocking out cells were purchased from Horizon Discovery. Knockdown of MAZ in K562 cells was conducted by using an electroporation system. SiRNAs against MAZ were On-TARGET plus SMARTpool siRNA oligonucleotides purchased from Dhmarcon Inc.
|
| 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.
ChIP-Seq libraries were prepared using the “NEBNext® Ultra™ II DNA Library Prep Kit”. MeDIP-Seq libraries were prepared using MagMeDIP-seq Package V2 MeDIP-seq library prep. kit. RNA-Seq Libraries were prepared with NEBNext® UltraTM Directional RNA Library Prep Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Input
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
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: Reads were mapped to hg19 whole genome using bowtie2. Peaks were called using MACS2. Bigwig files were generated with Deeptools.
Supplementary files format and content: Processed data files are in bigwig format
|
| |
|
| Submission date |
Feb 21, 2024 |
| 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 |
SAMN40013675 |
| SRA |
SRX23678726 |
