Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
STAT3

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

ENA-CHECKLIST
ERC000011
ENA-FIRST-PUBLIC
2020-07-06
ENA-LAST-UPDATE
2019-10-08
External Id
SAMEA6059155
INSDC center alias
3. Department of General Surgery, Shanghai Sixth People’s Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai, 201308, China
INSDC center name
3. Department of General Surgery, Shanghai Sixth People’s Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai, 201308, China
INSDC first public
2020-07-06T04:03:41Z
INSDC last update
2019-10-08T10:56:39Z
INSDC status
public
SRA accession
ERS3860284
Sample Name
E-MTAB-8417:mutant_2_stat3
Submitter Id
E-MTAB-8417:mutant_2_stat3
broker name
ArrayExpress
cell_line
SW480
cell_type
epithelial cell of large intestine
common name
human
developmental stage
adult
disease
colorectal carcinoma
genotype
STAT3 knockout
isolate
not applicable
organism part
colon
title
mutant_2_stat3

Sequenced DNA Library

library_name
mutant_2_stat3_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
SW480 cells were edited by CRISPR-CAS9 for the residue 400 to 411 (\"NNGSLSAEFKHL\") of Stat3 deletion. 10% whole cell lysates were saved as input after genomic DNA was broken into 200-500 bp by sonication. 1 μg IP grade antibodies of STAT3 were incubated with the rest of the lysate overnight, followed by 2 h protein-A beads incubation at 37 °C for target protein pull down. The STAT3 enriched DNA or input DNA were repaired to 3'-dA overhang and added the ligated adapter. 0.2 ug of pull down DNA sample was submitted to NOVOGENE (Beijing, China) for library generation and sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
20079109
Reads aligned (%)
94.2
Duplicates removed (%)
2.8
Number of peaks
1437 (qval < 1E-05)

hg38

Number of total reads
20079109
Reads aligned (%)
96.2
Duplicates removed (%)
1.7
Number of peaks
1599 (qval < 1E-05)

Base call quality data from DBCLS SRA