SRX100412
GSM803367: HudsonAlpha ChipSeq HepG2 TAF1 PCR2x

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TAF1

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 (p250). Antibody Target: TAF1
antibody targetdescription
TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.
antibody vendorname
Santa Cruz Biotechnology
antibody vendorid
sc-735
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
SL358,SL359
replicate
1,2
softwareversion
MACS
antibody targetdescription
TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.
antibody vendorname
Santa Cruz Biotech
antibody vendorid
sc-735
treatment
None
treatment description
No special treatment or protocol applies
protocol
PCR2x
protocol description
2-cycles of PCR (Myers)
controlid
SL294
labexpid
SL358
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803367: HudsonAlpha_ChipSeq_HepG2_TAF1_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
76594558
Reads aligned (%)
58.6
Duplicates removed (%)
16.8
Number of peaks
25674 (qval < 1E-05)

hg19

Number of total reads
76594558
Reads aligned (%)
58.2
Duplicates removed (%)
17.4
Number of peaks
26529 (qval < 1E-05)

Base call quality data from DBCLS SRA