Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RNF2

Cell type

Cell type Class
Others
Cell type
Mesenchymal stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
Bone marrow derived hMSC
cell type
human Mesenchymal Stem Cells
passages
p4-p10
chip antibody
anti-RNF2 (NAST)RRID:AB_2755047

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were processed for ChIP as previously described with slight modifications (Dietrich, Lerdrup et al., 2012). Briefly, cells were fixed for 10 min in culture media containing 1% formaldehyde and were processed for ChIP as previously described with slight modifications (Dietrich et al., 2012). ChIP DNA from three parallel ChIPs were pooled or individual ChIPs from three biological replicates were used and 10 ng each was used for making ChIP-seq libraries. The libraries were prepared using “ChIP seq DNA sample preparation kit” from Illumina following manufacturer's instructions. H3K27ac samples were multiplexed (using NEB kit) and run on HiSeq2000 (Illumina).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
40326085
Reads aligned (%)
83.8
Duplicates removed (%)
11.4
Number of peaks
1455 (qval < 1E-05)

hg38

Number of total reads
40326085
Reads aligned (%)
86.2
Duplicates removed (%)
9.8
Number of peaks
1232 (qval < 1E-05)

Base call quality data from DBCLS SRA