Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MECP2

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
HCT116_MeCP2
cell line
HCT116
chip antibody
MeCP2 (Abcam; ab2828)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from 5 million cells per ChIP was prepared by formaldehyde cross-linking and sonication as described previously. Antibodies against MeCP2 (Abcam; ab2828) and ser2p-PolII (Abcam; ab5095) were added in manufacturer-recommended amounts per ChIP. For input control samples, DNA was isolated from 10% (vol.) of chromatin material used for ChIP by phenol/chloroform extraction and ethanol purification procedures. ChIP-Seq was carried out according to established protocols and prepared libraries were sequenced with the Illumina Genome Analyzer II or HiSeq 2000 sequencer according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
29735259
Reads aligned (%)
26.4
Duplicates removed (%)
71.7
Number of peaks
1022 (qval < 1E-05)

hg38

Number of total reads
29735259
Reads aligned (%)
28.0
Duplicates removed (%)
70.2
Number of peaks
1088 (qval < 1E-05)

Base call quality data from DBCLS SRA