Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GTF2I

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
Fibroblast-derived iPSC
genotype
Control
donor
GDB-339-1
gender
female
chip antibody
GTF2I (Cell Signalling 4562S)
flowcell id
D21AKACXX

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer specifications. About 10^8 iPSCs have been cross linked for 10 minutes in PBS containing 1% formaldehyde at room temperature. Crosslinking was quenched adding Glycine to a final concentration of 125mM for 5 minutes at room temperature. Cells nuclei were lysed using ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and sonicated using the Covaris Sonicator (see sample description) to obtain a sheared chromatin DNA bulk of 250 bp. Sheared chromatin was incubated with GTF2I (15ug) or LSD1 (10ug) antibodies overnight rotating at 4 degree. The day after the antibody was recovered using Dynabeads Protein G (Life Technologies) and washed 4 times using washing buffers. Finally DNA was eluted using SDS containing elution buffer and decrossliked overnight at 65 degree. The third day decrosslinked DNA was digested using proteinase K for 60 minutes at 45 degree and purified using DNA-purification columns (Qiagen).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
31256162
Reads aligned (%)
84.3
Duplicates removed (%)
11.5
Number of peaks
1109 (qval < 1E-05)

hg38

Number of total reads
31256162
Reads aligned (%)
86.0
Duplicates removed (%)
10.5
Number of peaks
987 (qval < 1E-05)

Base call quality data from DBCLS SRA