Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TCF7L1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA

Attributes by original data submitter

Sample

source_name
H9 human ES cells
cell type
H9 human embryonic stem cells (passage 44)
cell state
Undifferentiated
antibody
TCF7L1 (Santa Cruz, sc-8635)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were isolated and treated with micrococcal nuclease (2,000 U/ul) for 25 minutes at 37 degrees to digest chromatin. Nuclie were briefly sonicated, clarifed and then TCF7L1-DNA complexes were isolated by immunoprecipitation. Illumina sequencing libraries were constructed using the Bioo Scientific NEXTflex Rapid DNA-Seq kit and NEXTflex DNA barcodes (Bioo Scientific Corporation, Austin TX). Ten nanograms of input DNA was taken into end repair, adenylation and adapter ligation reactions. The adapter ligated product was cleaned up without library size selection using Agencourt AMPure XP beads (Beckman Coulter, Inc. Brea, CA). The cleaned ligated DNA was amplified by 15 PCR cycles to enrich for adapter ligated products. The amplified PCR product was cleaned by AMPure XP beads and the library was size selected using the Blue Pippin 2% agarose gel with broad range settings (206bp – 561bp) (Sage Science, Inc. Beverly, MA). The libraries were quantified by Kapa qPCR (Kapa Biosystems, Inc. Wilmington, MA). The libraries were denatured and diluted to 13pM for onboard clustering on the Illumina HiSeq 2500 (Illumina Inc., San Diego, CA) using rapid run mode and SR50 chemistry. The HiSeq 2500 real time analysis software was version 1.17.21.3 and the HiSeq control software version was 2.0.10.0.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
66481032
Reads aligned (%)
46.6
Duplicates removed (%)
50.3
Number of peaks
449 (qval < 1E-05)

hg38

Number of total reads
66481032
Reads aligned (%)
47.8
Duplicates removed (%)
49.3
Number of peaks
353 (qval < 1E-05)

Base call quality data from DBCLS SRA