Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXF1

Cell type

Cell type Class
Digestive tract
Cell type
GIST48
NA
NA

Attributes by original data submitter

Sample

source_name
GIST48-siSCR-FOXF1
cell line
GIST48

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
GIST cells were transfected with siRNAs using DharmaFECT2 (GE healthcare) according to the manufacture's protocol. In brief, transfection was performed under serum free conditions, using 20nM siRNA in Opti-MEM. cells were crosslinked for 15 min in 1% paraformaldehyde, washed and lysed. Chromatin was sheared using Bioruptor (Diagenode) to fragments of approximately 150 base pairs and was incubated with anti-rabbit IgG Dynabeads (Invitrogen) pre-conjugated with primary antibody,  ChIP libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
85023636
Reads aligned (%)
87.8
Duplicates removed (%)
6.0
Number of peaks
6831 (qval < 1E-05)

hg38

Number of total reads
85023636
Reads aligned (%)
90.3
Duplicates removed (%)
4.6
Number of peaks
7093 (qval < 1E-05)

Base call quality data from DBCLS SRA