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

source_name
SK-N-SH
biomaterial_provider
ATCC
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
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.
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
SL108,SL410
labexpid
SL83,SL409
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
SL108
labexpid
SL83
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803335: HudsonAlpha_ChipSeq_SK-N-SH_NRSF_PCR2x
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
80466820
Reads aligned (%)
43.9
Duplicates removed (%)
8.7
Number of peaks
36889 (qval < 1E-05)

hg38

Number of total reads
80466820
Reads aligned (%)
44.2
Duplicates removed (%)
8.3
Number of peaks
37040 (qval < 1E-05)

Base call quality data from DBCLS SRA