Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
NCCIT
Primary Tissue
Testis
Tissue Diagnosis
Teratoma

Attributes by original data submitter

Sample

source_name
NCCIT cell line (human embryonic carcinoma)
biomaterial_provider
ATCC CRL-2073
cell line
NCCIT
cell type
Human embryonal carcinoma
chip antibody
H3K4me3 (Active Motif 39159)
grna target
None
grna scaffold species
None
dcas9 fusion expressed
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP assays were performed as described previously (Rada-Iglesias et al., 2011). Briefly, approximately 10&7 NCCIT cells were fixed in 1% formaldehyde for 10 minutes at room temperature in PBS, then quenched with glycine to a final concentration of 0.125 M for 10 minutes. Chromatin was sonicated to 0.5-2.0 kb using Bioruptor (Diagenode, Liège, Belgium), cleared by centrifugation, divided into separate aliquots for each antibody, and incubated with 5 mg of antibody overnight at 4° C. Subsequently, 100 mL of Dynabeads protein G (Thermo Fisher Scientific) were added to the ChIP reactions and incubated for 4-6 hours at 4° C. Magnetic beads were washed and chromatin was eluted, followed by reversal of crosslinks overnight at 65° C, proteinase K and RNase A treatment, and DNA purification by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. ChIP DNA was resuspended in water. Libraries were prepared using Ovation Ultralow System V2 UDI (NuGEN Technologies, San Carlos, CA, USA) according to manufacturer's instructions, starting with 10 ng of ChIP DNA. Library DNA was analyzed on Bioanalyzer DNA HS (Agilent, Santa Clara, CA, USA), then pooled and sequenced on a HiSeq 4000 (Illumina, San Diego, CA, USA) at the Stanford Genome Sequencing Service Center, using 2x150 sequencing with dual index read.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
27501479
Reads aligned (%)
92.8
Duplicates removed (%)
20.8
Number of peaks
28331 (qval < 1E-05)

hg19

Number of total reads
27501479
Reads aligned (%)
92.5
Duplicates removed (%)
20.8
Number of peaks
28055 (qval < 1E-05)

Base call quality data from DBCLS SRA