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Install and launch IGV before selecting data to visualize
For mm10
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For mm9
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
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Analyze
For mm10
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
For mm9
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
Download
For mm10
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For mm9
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
Link Out
Sequence Read Archive
DBCLS SRA
NCBI SRA
ENA
Antigen: Input control
wikigenes
PDBj
CellType: ES cells
ATCC
MeSH
RIKEN BRC
SRX589568
GSM1409783: RA WT Input; Mus musculus; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Input control
Antigen
Input control
Cell type
Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA
Attributes by original data submitter
Sample
source_name
WT_Retinoic acid treated ES cells
strain
mixed C57BL/6 CD1
genotype/variation
Utx fl/fl, Jmjd3 fl/fl, CreER
treated with
retinoic acid (2D)
cell type
Retinoic acid treated ES cells
passages
passage 9
chip antibody
Input
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were trypsinized, then fixed in 0.6% Formaldehyde. Cells were sonicated, then antibody ChIP. DNA was end repaired, A-tailed, then Illumina barcode adaptors were ligated and amplified.
Sequencing Platform
instrument_model
Illumina HiSeq 2000
Where can I get the processing logs?
Read processing pipeline
log
mm10
Number of total reads
8844857
Reads aligned (%)
98.2
Duplicates removed (%)
11.6
Number of peaks
336 (qval < 1E-05)
mm9
Number of total reads
8844857
Reads aligned (%)
97.9
Duplicates removed (%)
11.8
Number of peaks
336 (qval < 1E-05)
Base call quality data from
DBCLS SRA