Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
OTX2

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
neural precursor cell: neuroepithelial
cell type
ES-derived neural progenitor cells
genetic background
HES5::eGFP BAC transgenic human ES cells (H9; WA-09; Wicell) expressing GFP under the HES5 promoter
chip-antibody
Abcam,Ab21990,GR139309-4

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP_Seq:To extract DNA and create the Illumina library we used AMPure XP beads (Agencourt) Solid-phase reversible immobilization (SPRI). SPRI beads were added to the samples, mixed 15 times, incubated at room temperature for 2 minutes. Supernatant was extracted from the beads from the beads 4 minutes on a magnet. We used 70% ethanol to wash the beads and then dried for 4 minutes. 40 ul EB buffer (10 mM Tris-HCl pH 8.0) was used to elute the DNA. ChIP_Seq:The following steps of Illumina library construction (end-repair, addition of A-base, ligation of barcoded adaptors and PCR enrichment) we used a general SPRI cleanup procedure: addition of PEG buffer (20% PEG and 2.5 M NaCl), and extracted and washed as above. The enzymatic reactions were carried as follows: 1. DNA end-repair: T4 PNK and T4 polymerase (New England Biolabs) incubated 12C for 15 min, 25C for 15 min; 2. A-base addition: Klenow (3’->5’ exonuclease; New England Biolabs) incubated at 37C for 30 min. 3. Adaptor ligation: DNA ligase (New England Biolabs) and indexed oligo adaptors and incubated 25C for 15 min, followed by 0.7X SPRI/reaction to remove non-ligated adaptors. 4. PCR enrichment: PCR mastermix (primer set, dNTP mix, Pfu Ultra Buffer (Agilent), Pfu Ultra-II Fusion (Agilent), water), for 20 cycles. The PCR amplified libraries we cleaned up using 0.7X SPRI/reaction (size selection mode) to remove excessive primers. Roughly 5 picomoles of DNA library was then applied to each lane of the flow cell and sequenced on Illumina HiSeq 2000 sequencers according to standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
7690504
Reads aligned (%)
142.7
Duplicates removed (%)
15.8
Number of peaks
1338 (qval < 1E-05)

hg38

Number of total reads
7690504
Reads aligned (%)
143.9
Duplicates removed (%)
15.7
Number of peaks
1331 (qval < 1E-05)

Base call quality data from DBCLS SRA