SRX100414
GSM803369: HudsonAlpha ChipSeq PFSK-1 NRSF PCR2x

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
REST

Cell type

Cell type Class
Neural
Cell type
PFSK-1
Primary Tissue
Brain
Tissue Diagnosis
Medulloblastoma

Attributes by original data submitter

Sample

source_name
PFSK-1
biomaterial_provider
ATCC
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433)
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
SL150,SL412
labexpid
SL411,SL149
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
SL150
labexpid
SL149
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803369: HudsonAlpha_ChipSeq_PFSK-1_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
66387093
Reads aligned (%)
46.7
Duplicates removed (%)
11.6
Number of peaks
22830 (qval < 1E-05)

hg19

Number of total reads
66387093
Reads aligned (%)
46.5
Duplicates removed (%)
12.0
Number of peaks
22852 (qval < 1E-05)

Base call quality data from DBCLS SRA