Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
HRPEpiC
Tissue
epithelium
Lineage
ectoderm
Description
retinal pigment epithelial cells

Attributes by original data submitter

Sample

source_name
hTERT-Immortalized Retinal Pigment Epithelial Cells
cell type
hTERT-Immortalized Retinal Pigment Epithelial Cells
genotype
Input
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, 3 replicate pellet were prepared for each sample. Pellets consisted of at least 5 million cells, cross linked with 1% formaldehyde in phosphate buffered saline for 7 minutes before quenching with 125mM glycine for 5 minutes. Cells were pelleted before flash freezing and storing at -80C. Pellets were then shipped on dry ice to Zymo Research for ChIP preparation. For RNA-Seq, total RNA was extracted from three replicate cultures of each sample using the Machery Nagel Nucleospin RNA Plus kit according to the manufacturers recommendations. RNA samples were shipped on dry ice to Novogene Corporation for quality control analysis followed by rRNA depleted total RNA-Seq. Libraries for ChIP-Seq and RNA-Seq were prepared using the services provided by Zymo Research and Novogene Corporation respectively.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
47869184
Reads aligned (%)
97.6
Duplicates removed (%)
4.8
Number of peaks
1742 (qval < 1E-05)

hg19

Number of total reads
47869184
Reads aligned (%)
96.6
Duplicates removed (%)
6.1
Number of peaks
1452 (qval < 1E-05)

Base call quality data from DBCLS SRA