Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MBD4

Cell type

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

Attributes by original data submitter

Sample

GEO Accession
GSM1010740
antibody antibodydescription
Mouse monoclonal IgG, specific for an epitope mapping between a.a. 515-555 within an internal region of MBD4 of mouse origin. Antibody Target: MBD4
antibody targetdescription
MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq)
antibody vendorid
sc-271530
antibody vendorname
Santa Cruz Biotechnology
antibody
MBD4_(SC-271530)
cell description
hepatocellular carcinoma
cell karyotype
cancer
cell lineage
endoderm
cell organism
human
cell sex
M
cell
HepG2
controlid
SL6019
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL8132,SL7901
protocol description
Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)
protocol
v042211.1
replicate
1,2
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010740: HudsonAlpha_ChipSeq_HepG2_MBD4_(SC-271530)_v042211.1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
88547295
Reads aligned (%)
81.1
Duplicates removed (%)
6.9
Number of peaks
14627 (qval < 1E-05)

hg38

Number of total reads
88547295
Reads aligned (%)
82.5
Duplicates removed (%)
5.9
Number of peaks
15243 (qval < 1E-05)

Base call quality data from DBCLS SRA