|
Status |
Public on Jan 23, 2018 |
Title |
MCRS1 HepG2 A |
Sample type |
SRA |
|
|
Source name |
HepG2
|
Organism |
Homo sapiens |
Characteristics |
cell type: liver cancer cell line cell line: HepG2 antibody: MCRS1 vendor: protein-tech catalog number: 11362-1-AP lot: 1 treatment: None
|
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 |
Reanalysis of GSM2564079
|
Data processing |
Align bowtie2 --sensitive samtools rmdup samtools merge bamCoverage --binSize 10 --extendReads 150 --normalizeUsingRPKM --centerReads 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 signal tracks Supplementary_files_format_and_content: bed files = peaks called from merged replicates of bam files for INO80 subunits in 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 |
Dec 05, 2017 |
Last update date |
May 15, 2019 |
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 (1) |
GSE107730 |
Genomic occupancy of the INO80 complex [II] |
|
Relations |
Alternative to |
GSM2564079 |
BioSample |
SAMN08134955 |
SRA |
SRX3445802 |