SRX190240
GSM1010784: HudsonAlpha ChipSeq HepG2 NRSF v041610.1

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

GEO Accession
GSM1010784
antibody antibodydescription
Mouse monoclonal. Antibody Target: NRSF
antibody targetdescription
Neuron-restrictive silencer transcription factor
antibody vendorid
(Made by Protein Expression Center: pec@caltech.edu)
antibody vendorname
David Anderson, Caltech
antibody
NRSF
cell description
hepatocellular carcinoma
cell karyotype
cancer
cell lineage
endoderm
cell organism
human
cell sex
M
cell
HepG2
controlid
SL3976
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL5897,SL5040
protocol description
2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)
protocol
v041610.1
replicate
1,2
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010784: HudsonAlpha_ChipSeq_HepG2_NRSF_v041610.1
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

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
75401789
Reads aligned (%)
84.9
Duplicates removed (%)
16.7
Number of peaks
17873 (qval < 1E-05)

hg19

Number of total reads
75401789
Reads aligned (%)
84.3
Duplicates removed (%)
17.7
Number of peaks
17784 (qval < 1E-05)

Base call quality data from DBCLS SRA