Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MED1

Cell type

Cell type Class
Liver
Cell type
HuCCT1
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
HuCCT1 human cell line
cell line
HuCCT1
sirna
Control
chip antibody
MED1 (Bethyl, catalog# A300-793A, lot# A300-793A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature after which the reaction was stopped by addition of 0.125M glycine. Cells were lysed and harvested in ChIP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100 and 5 mM EDTA) and the chromatin disrupted by sonication using a Diagenode Bioruptor sonicator UCD-200 to obtain fragments of 200-500 bp in size. Suitable amounts of chromatin were incubated with specific antibodies overnight. Antibodies used are: H3K4Me3 (Millipore – Cat. # 07-473), H3K27Ac (Abcam – Cat. # ab4729), H3K4Me1 (Abcam – Cat. # ab8895), MED1 (Bethyl – Cat. # A300-793A), SMC1 (Bethyl – Cat. # A300-005A), Pol2 (Santa Cruz – Cat. # sc-899), Phospho-Rpb1 CTD (Ser2) (Cell Signaling – Cat. # 13499), Phospho-Rpb1 CTD (Ser5) (Cell Signaling – Cat. # 13523), CDK9 (Santa Cruz – Cat. # sc-484) Libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina and barcoded using NEBNext Multiplex Oligos for Illumina according to manufacturer recommendation.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
51242686
Reads aligned (%)
78.6
Duplicates removed (%)
18.9
Number of peaks
18551 (qval < 1E-05)

hg38

Number of total reads
51242686
Reads aligned (%)
79.8
Duplicates removed (%)
18.1
Number of peaks
18658 (qval < 1E-05)

Base call quality data from DBCLS SRA