Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CBX3

Cell type

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

Attributes by original data submitter

Sample

GEO Accession
GSM1010758
antibody antibodydescription
Mouse monoclonal IgG, raised against recombinant CBX3 of human origin. Antibody Target: CBX3
antibody targetdescription
At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene.
antibody vendorid
sc-101004
antibody vendorname
Santa Cruz Biotechnology
antibody
CBX3_(SC-101004)
cell description
colorectal carcinoma (PMID: 7214343)
cell karyotype
cancer
cell lineage
endoderm
cell organism
human
cell sex
M
cell
HCT-116
controlid
SL12247,SL12246
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL12229,SL13066
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
GSM1010758: HudsonAlpha_ChipSeq_HCT-116_CBX3_(SC-101004)_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
60614219
Reads aligned (%)
87.6
Duplicates removed (%)
5.5
Number of peaks
67608 (qval < 1E-05)

hg38

Number of total reads
60614219
Reads aligned (%)
88.4
Duplicates removed (%)
5.0
Number of peaks
67623 (qval < 1E-05)

Base call quality data from DBCLS SRA