Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
REST

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

GEO Accession
GSM1010891
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
mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis
cell karyotype
cancer
cell lineage
ectoderm
cell organism
human
cell sex
F
cell
MCF-7
controlid
SL13504
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL14698,SL13491
protocol description
Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)
protocol
v042211.1
replicate
1,2
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010891: HudsonAlpha_ChipSeq_MCF-7_NRSF_v042211.1
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
59354697
Reads aligned (%)
82.4
Duplicates removed (%)
12.2
Number of peaks
14691 (qval < 1E-05)

hg38

Number of total reads
59354697
Reads aligned (%)
83.7
Duplicates removed (%)
11.2
Number of peaks
14347 (qval < 1E-05)

Base call quality data from DBCLS SRA