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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)
Error connecting to IGV?
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: Hdac1
wikigenes
PDBj
CellType: ES cells
ATCC
MeSH
RIKEN BRC
SRX823817
GSM1572672: R-EtOH-HDAC1-rep1; Mus musculus; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
Hdac1
Cell type
Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA
Attributes by original data submitter
Sample
source_name
R-EtOH-HDAC1
strain background
C57BL/6
genotype/variation
Foxd3 conditional knockout
cell type
ESCs (R cells)
cell line of origin
embryonic stem cells: ESCs (R cells)
treatment
Lif 2i
chip antibody
HDAC1
chip antibody vendor
Abcam
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNA was extracted using a standard ChIP protocol Library was constructed using a standard Illumina protocol
Sequencing Platform
instrument_model
Illumina HiSeq 2000
Where can I get the processing logs?
Read processing pipeline
log
mm10
Number of total reads
24247326
Reads aligned (%)
83.8
Duplicates removed (%)
86.4
Number of peaks
159 (qval < 1E-05)
mm9
Number of total reads
24247326
Reads aligned (%)
83.6
Duplicates removed (%)
86.6
Number of peaks
175 (qval < 1E-05)
Base call quality data from
DBCLS SRA