GSM1239407: batch3 chrom1 LoVo HNF1A Rabbit PassedQC; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
HNF1A
Cell type
Cell type Class
Digestive tract
Cell type
LoVo
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma
Attributes by original data submitter
Sample
source_name
LoVo
cell line
LoVo
cell type
colon adenocarcinoma
hgn
HNF1A
antibody
Santa Cruz Biotechnology, Inc. : sc-10791 X
control sample
batch3_chrom1_LoVo_IgG_Rabbit
qc successful
PassedQC
fraction of peaks close to tss
0.098901
lowest e-value for a high complexity de novo motif
5.6e-13
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit. Libraries were constructed according to Illuminas standard protocol. The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane. Sequencing was performed using one lane of Illumina GAIIx, or alternatively, samples were indexed with DNA barcodes and four to six different samples were multiplexed in one library and sequenced using Illumina HiSeq 2000 (single 36 bp reads).