|
| Status |
Public on Oct 20, 2020 |
| Title |
SAHA_H4ac_Rep2_and_H3K27ac_ChIP_Input |
| Sample type |
SRA |
| |
|
| Source name |
HL60
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: leukemia cell line HL60
chip antibody: none
treatment: SAHA
spike-in genome: dm3
|
| Treatment protocol |
HL60 cells were treated with either DMSO or SAHA for 1hr or 2hr prior to collection
|
| Growth protocol |
Cells were grown in RPMI-1640 plus 20% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted using TRIzol reagent. For H4ac ChIP, HL60 cells were cultured to a density of 7x10^5 cell/mL and treated with 1 µM SAHA or 0.01% DMSO for 1 h prior to ChIP protocol.
Sequencing libraries were generated from DNA enriched by ChIP following the manufacturer’s specification for the Tru-Seq library preparation kit (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
For H4ac ChIP, single end 50-bp reads were filtered using TagDust (Lassmann et al. 2009). ChIP-Rx normalization was performed as described in (Orlando et al. 2014). Briefly, reads were first aligned to the Drosophila dm3 genome using Bowtie (Langmead et al. 2009). Unmapped reads were then aligned to the human hg19 genome using Bowtie and reads were normalized to Drosophila mapped read counts.
To generate differential windows, input signal was subtracted from ChIP signal. Signal was then averaged across 300bp sliding windows offset by 100 bp. Differential windows were identified using DESEQ2 (Love et al. 2014). Windows with significant enrichment were merged and identified as a peak.
For BRD4 ChIP, single end 50-bp reads were filtered using TagDust (Lassmann et al. 2009) and aligned to hg19 using Bowtie (Langmead et al. 2009). Peaks were called with MACS2 (Zhang et al. 2008).
Sequencing reads were aligned to hg19 (STAR v2.5.2b, (Dobin et al. 2013). Differential genes were identified by DESEQ2 (Love et al. 2014) and count data was used to generate the MAplot using RStudio.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files represent spike-in normalized read depth genomic coverage
Excel files contain peak calls as determined by MACS2
DESeq2 differential gene files contain relevant data necessary to determine differential genes via DESeq2
ROSE super-enhancer files lists enhancer, super-enhancers, and signal associated with called enhancers
Differential window files contain differential H4ac peaks as determined by DESeq2
The combined expression matrix contains the TPMs (as calculated by Salmon) for each RefSeq isoform across all samples.
|
| |
|
| Submission date |
Oct 19, 2020 |
| Last update date |
Oct 20, 2020 |
| Contact name |
Austin J Hepperla |
| E-mail(s) |
hepperla@unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Street address |
7018B Mary Ellen Jones Building
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE159620 |
HDAC inhibitors result in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies |
|
| Relations |
| BioSample |
SAMN16477818 |
| SRA |
SRX9309777 |
