GSM1239428: batch3 chrom2 LoVo LHX4 Goat FailedQC; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
LHX4
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
LHX4
antibody
Santa Cruz Biotechnology, Inc. : sc-22138 X
control sample
batch3_chrom2_LoVo_IgG_Goat
qc successful
FailedQC
fraction of peaks close to tss
0.053456
lowest e-value for a high complexity de novo motif
0.36
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).