Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PBX3

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
GSM1010887
antibody antibodydescription
Rabbit Polyclonal IgG. Antibody Target: PBX3
antibody targetdescription
Pbx 3 (D-17)
antibody vendorid
sc-891
antibody vendorname
Santa Cruz Biotechnology
antibody
Pbx3
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
SL16761,SL13505
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL16042,SL13495
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
GSM1010887: HudsonAlpha_ChipSeq_SK-N-SH_Pbx3_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
80798079
Reads aligned (%)
79.3
Duplicates removed (%)
12.2
Number of peaks
80140 (qval < 1E-05)

hg38

Number of total reads
80798079
Reads aligned (%)
80.6
Duplicates removed (%)
11.2
Number of peaks
80336 (qval < 1E-05)

Base call quality data from DBCLS SRA