|
| Status |
Public on Apr 01, 2020 |
| Title |
RUVBL1_HepG2_A |
| Sample type |
SRA |
| |
|
| Source name |
RUVBL1_HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: liver cancer cell line
chip antibody: RUVBL1
chip antibody vendor: bethyl
chip antibody cat. #: ab51500
lot: A304-716A-T-1
|
| Treatment protocol |
In experiments with drug treamtne (EPZ-6438 or DMSO at 1.0uM ) was added to cells for 120 hours prior to fixing for ChIP.
|
| Growth protocol |
Cells were grown in DMEM + 10% FBS + penicillin + streptomycin at 37 degrees in 5% C02. Experiments were performed on cells less than 10 passages.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees prior to processing for ChIP using protocol from Raab et al 2015.
Kapa Hyperprep kit using Illumina Truseq barcoded adapters
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file:
RUVBL1_HepG2_peaks.narrowPeak.filtered.fixed.txt
|
| Data processing |
Align bowtie2 --sensitive
samtools rmdup
samtools merge
bamCoverage --binSize 10 --extendReads 150 --normalizeUsingRPKM --centerReads (For drug treated samples additionally --scaleFactor was used with the normalization factor derived as 1/#of tags mapped against reference drosophila genome in millions - file dtags_agg.csv
macs2 callpeak -q 0.001 --keep-dup all --shift 37 --nomodel --extsize 147 -g hs
peaks were filtered against blacklist (ENCODE) using bedtools and recursviely merged with other peaks within 500bp to yield final peak calls
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files = Reads per million (no treatment samples) or reference normalized reads per million (DMSO/EPZ64-38 treated) signal tracks
Supplementary_files_format_and_content: bed files = peaks called from merged replicates of bam files for INO80 subunits in Huh7 and HepG2
Supplementary_files_format_and_content: raw files ending in rmdup.dtags.bam were aligned against dm3 to count the total number of non-duplicate uniquely mapping drosohpila reads in each IP sample and used for normalization - count values are in dtags_agg.csv
|
| |
|
| Submission date |
Apr 05, 2017 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Jesse Raab |
| E-mail(s) |
jesse.r.raab@gmail.com
|
| Organization name |
University of North Carolina Chapel Hill
|
| Department |
Genetics
|
| Street address |
120 Mason Farm Rd
|
| City |
Chapel Hill |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE97411 |
Genomic occupancy of the INO80 complex [ChIP-seq] |
| GSE97413 |
INO80 complex assembly is antagonized by PRC2. |
|
| Relations |
| Alternative to |
GSM2877264 |
| BioSample |
SAMN06688230 |
| SRA |
SRX2708822 |
