SRX100388
GSM803343: HudsonAlpha ChipSeq HepG2 GABP PCR2x

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GABPA

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
biomaterial_provider
ATCC
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
hepatocellular carcinoma
antibody antibodydescription
Mouse monoclonal, GABPa(G-1), IgG1. Antibody Target: GABP
antibody targetdescription
The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence.
antibody vendorname
Santa Cruz Biotechnology
antibody vendorid
sc-28312
protocol description
a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)
controlid
SL295,SL294
labexpid
SL275,SL276
labversion
SL275
replicate
1,2
softwareversion
MACS
antibody vendorname
Santa Cruz Biotech
antibody vendorid
sc-28312
treatment
None
treatment description
No special treatment or protocol applies
protocol
PCR2x
protocol description
2-cycles of PCR (Myers)
controlid
SL294
labexpid
SL275
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803343: HudsonAlpha_ChipSeq_HepG2_GABP_PCR2x
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
99783736
Reads aligned (%)
63.3
Duplicates removed (%)
41.1
Number of peaks
20792 (qval < 1E-05)

hg19

Number of total reads
99783736
Reads aligned (%)
63.0
Duplicates removed (%)
41.6
Number of peaks
21577 (qval < 1E-05)

Base call quality data from DBCLS SRA