Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
Human IPSCs
cell/region
hPSCs
chip antibody
H3K4me3Q5ser (Millipore 4491a; Lot#RA1608107)
differentiation status
Undifferentiated PSCs

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell pellets (>10 x 10^6/n) and brain tissues were crosslinked and quenched. Samples were washed thoroughly before being subjected to lysis and sonication. Samples were then incubated with specific antibodies (7.5 μg/sample) bound to M-280 Dynabeads on a rotator at 4°C overnight. The following day, immunoprecipitates were washed, eluted and reverse crosslinked. Following RNA and protein digestion, DNA fragments were purified using a Qiagen PCR purification kit. RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
43501199
Reads aligned (%)
97.2
Duplicates removed (%)
36.8
Number of peaks
1574 (qval < 1E-05)

hg19

Number of total reads
43501199
Reads aligned (%)
96.2
Duplicates removed (%)
38.2
Number of peaks
1445 (qval < 1E-05)

Base call quality data from DBCLS SRA