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Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
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For hg19
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
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For hg38
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For hg19
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
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Sequence Read Archive
DBCLS SRA
NCBI SRA
ENA
Antigen: PBX3
wikigenes
PDBj
CellType: SK-N-SH
ATCC
MeSH
RIKEN BRC
Variation
TogoVar
SRX190343
GSM1010887: HudsonAlpha ChipSeq SK-N-SH Pbx3 v042211.1
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
Where can I get the processing logs?
Read processing pipeline
log
hg38
Number of total reads
80798079
Reads aligned (%)
90.8
Duplicates removed (%)
11.2
Number of peaks
80336 (qval < 1E-05)
hg19
Number of total reads
80798079
Reads aligned (%)
90.3
Duplicates removed (%)
12.2
Number of peaks
80140 (qval < 1E-05)
Base call quality data from
DBCLS SRA