Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC1A

Cell type

Cell type Class
Liver
Cell type
Hep G2
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by original data submitter

Sample

source_name
HEPG2-CHIP-SMC1A
cell line
HEPG2 (ATCC, HB-8065)
cell type
Hepatocellular carcinoma-dirived cells
passages
N/A
treated with
none
chip antibody
SMC1 (Bethyl, A300-055A, lot:3)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde in culture medium for 10 minutes at room temperature. Cells were then lysed in 10 ml lysis buffer (0.1%SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl ph 8.0 and 150 mM NaCl) and chromatin was sheared to 200-600 bp fragments using a Bioruptor Sonicator (Diagenode). Chromatin extract from 5x10^7 cells was incubated overnight at 4oC with 100 ul of Dynabeads Protein G magnetic beads (Life Technologies, 10004D) previously incubated with 10 ug of selected antibodies. After ChIP, samples were washed and bound complex were reversed cross-linked and eluted in 10mM Tris-HCl pH 8 The TruSeq DNA sample prep kit with indexing adapters was used according to the manufacturer's recommendations (Illumina)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
24959688
Reads aligned (%)
92.1
Duplicates removed (%)
5.1
Number of peaks
35939 (qval < 1E-05)

hg38

Number of total reads
24959688
Reads aligned (%)
93.2
Duplicates removed (%)
4.5
Number of peaks
36008 (qval < 1E-05)

Base call quality data from DBCLS SRA