Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RING1

Cell type

Cell type Class
Epidermis
Cell type
Hs 68
Primary Tissue
Unknown
Tissue Diagnosis
Canavan disease

Attributes by original data submitter

Sample

source_name
Cultured fibroblasts
tissue
normal foreskin
chip antibody
2820 from Cell Signalling Lab, LRI
strain
Hs68

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow use of the Invitrogen SizeSelect E-gel system. Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip before clustering and subsequent 36bp single end sequencing on the GAIIx analyser. RNA-Seq: Total RNA was extracted using the High Pure RNA extraction Kit (Roche). RNA samples were quality controlled (QC) using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent) and subjected to poly-A selection using Sera-Mag oligo dT beads (Thermo Fisher Scientific Inc.). Libraries were prepared using the Directional mRNA-Seq Library Prep. v1.0. Pre-Release Protocol from Illumina with minor adjustments. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix which reduced the overall volume of the PCR and the ratio for the Agencourt AMPure XP beads was adjusted accordingly. The standard PCR cycling was also changed to match the concentration of the total RNA from the initial QC. After passing the final QC, the libraries were subjected to cluster formation and then 72bp single end sequencing on the GAIIx analyser.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
70065837
Reads aligned (%)
83.8
Duplicates removed (%)
5.3
Number of peaks
1734 (qval < 1E-05)

hg38

Number of total reads
70065837
Reads aligned (%)
84.9
Duplicates removed (%)
4.7
Number of peaks
2837 (qval < 1E-05)

Base call quality data from DBCLS SRA