Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
REST

Cell type

Cell type Class
Neural
Cell type
SK-N-SH
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

GEO Accession
GSM1010735
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
neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.
cell karyotype
cancer
cell lineage
ectoderm
cell organism
human
cell sex
F
cell
SK-N-SH
controlid
SL3774
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL5896,SL5494
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
GSM1010735: HudsonAlpha_ChipSeq_SK-N-SH_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

hg19

Number of total reads
62131282
Reads aligned (%)
65.0
Duplicates removed (%)
20.2
Number of peaks
22036 (qval < 1E-05)

hg38

Number of total reads
62131282
Reads aligned (%)
66.0
Duplicates removed (%)
19.4
Number of peaks
21613 (qval < 1E-05)

Base call quality data from DBCLS SRA