Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K36me3

Cell type

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

Attributes by original data submitter

Sample

source_name
iPSC-derived neural cells
tissue
iPSC-derived neural cells
genotype
Huntington's disease
chip antibody
H3K36me3 (Abcam cat #ab9050)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% (vol/vol) formaldehyde for 10 min, and the cross-linking was quenched by 0.125 M final concentration glycine. The cross-linked tissue was then homogenized, and rinsed with PBS, and frozen in liquid nitrogen. Later, Crosslinked tissues were fragmented to the size range of 100–500 bp using a Bioruptor (Bioruptor Next Gen; Diagenode). Antibodies for each mark were incubated with beads for 6 h before incubating with sonicated chromatin overnight. Resulting immunoprecipitated DNA was prepared for high-throughput sequencing using a library preparation kit from Beckman Coulter (catalog #A88267). Libraries were sequenced on an Illumina platform following the manufacturer’s standard protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
154925770
Reads aligned (%)
97.9
Duplicates removed (%)
12.2
Number of peaks
4377 (qval < 1E-05)

hg19

Number of total reads
154925770
Reads aligned (%)
97.3
Duplicates removed (%)
13.5
Number of peaks
3085 (qval < 1E-05)

Base call quality data from DBCLS SRA