Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9me3

Cell type

Cell type Class
Uterus
Cell type
Ishikawa
Primary Tissue
Uterus
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Ishikawa SID4x-dCas9-KRAB
antibody
H3K9me3
grna treatment
Enhancer-I
drug treatment
none
growth conditions
charcoal-stripped RPMI

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
20 million cells per ChIP were crosslinked in 1% formaldehyde for 10 minutes at room temperature. Crosslinking was stopped with 125 mM Glycine and nuclei were extracted. Chromatin was sonicated using an Epishear Probe Sonicator (Active Motif) for 3 minutes at 40% power. c-MYC (D3N8F) antibody (Cell Signaling Technology) was used for immunoprecipitation and an input sample for each cell line served as the control. Libraries were constructed using a standard Illumina library construction protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
22781600
Reads aligned (%)
94.0
Duplicates removed (%)
14.0
Number of peaks
1046 (qval < 1E-05)

hg19

Number of total reads
22781600
Reads aligned (%)
92.8
Duplicates removed (%)
16.4
Number of peaks
1110 (qval < 1E-05)

Base call quality data from DBCLS SRA