SRX100389
GSM803344: HudsonAlpha ChipSeq HepG2 NRSF PCR2x

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
REST

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. Antibody Target: NRSF
antibody targetdescription
Neuron-restrictive silencer transcription factor
antibody vendorname
Dr. David Anderson at Caltech
antibody vendorid
(Made by Protein Expression Center: pec@caltech.edu)
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
SL274,SL273
replicate
1,2
softwareversion
MACS
antibody targetdescription
Neuron-restrictive silencer transcription factor
antibody vendorname
David Anderson, Caltech
antibody vendorid
(Made by Protein Expression Center: pec@caltech.edu)
treatment
None
treatment description
No special treatment or protocol applies
protocol
PCR2x
protocol description
2-cycles of PCR (Myers)
controlid
SL294
labexpid
SL273
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803344: HudsonAlpha_ChipSeq_HepG2_NRSF_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
93711691
Reads aligned (%)
48.0
Duplicates removed (%)
16.6
Number of peaks
16964 (qval < 1E-05)

hg19

Number of total reads
93711691
Reads aligned (%)
47.7
Duplicates removed (%)
17.3
Number of peaks
17326 (qval < 1E-05)

Base call quality data from DBCLS SRA