Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MED1

Cell type

Cell type Class
Others
Cell type
Mesenchymal stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
BM-hMSC-TERT4 osteoblast diff 1d
cell line
BM-hMSC-TERT4
differentiation status
osteoblast
timepoint
1d
chip antibody
MED1 (M-255, sc-8998, Santa Cruz)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was prepared from 150 mm culture dishes first by crosslinking in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 0.125 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH=8) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 1.5 ml in 15-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279). Chromatin used for ChIP-seq of MED1 was also cross-linked in 2 mM disuccinimidyl glutarate (DSG) for 20 minutes at RT prior to cross-linking with formaldehyde. DNase-seq and ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg19

Number of total reads
21334483
Reads aligned (%)
71.7
Duplicates removed (%)
26.9
Number of peaks
12755 (qval < 1E-05)

hg38

Number of total reads
21334483
Reads aligned (%)
73.4
Duplicates removed (%)
25.7
Number of peaks
12707 (qval < 1E-05)

Base call quality data from DBCLS SRA