Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TAF1

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
GSM1010773
antibody antibodydescription
Mouse monoclonal (p250). Antibody Target: TAF1
antibody targetdescription
TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.
antibody vendorid
sc-735
antibody vendorname
Santa Cruz Biotechnology
antibody
TAF1
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
SL2134
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL6462,SL5612
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
GSM1010773: HudsonAlpha_ChipSeq_SK-N-SH_TAF1_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
80444913
Reads aligned (%)
58.8
Duplicates removed (%)
25.9
Number of peaks
18902 (qval < 1E-05)

hg38

Number of total reads
80444913
Reads aligned (%)
60.3
Duplicates removed (%)
24.5
Number of peaks
19056 (qval < 1E-05)

Base call quality data from DBCLS SRA