Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived neural crests
NA
NA

Attributes by original data submitter

Sample

source_name
Cranial neural crest cells
individual
1
cell type
Cranial neural crest cells (CNCCs)
cnccs derived from
H9 (ESC)
chip antibody
anti-H3K4me1 (Abcam, ab8895, catalog# lot# GR149140-2)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIPs were performed using approximately 0.5-1 x 10^7 CNCCs fixed with 1% formaldehyde for 10 min at room temp. RNA was extracted using Trizol. Sequencing libraries were prepared starting from ~30ng of ChIP DNA or oligo-dT purified mRNA using the NEBNext Multiplex Oligos for Illumina kit (Cat# E7335S).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
25043713
Reads aligned (%)
98.4
Duplicates removed (%)
17.7
Number of peaks
37237 (qval < 1E-05)

hg19

Number of total reads
25043713
Reads aligned (%)
98.2
Duplicates removed (%)
17.8
Number of peaks
37175 (qval < 1E-05)

Base call quality data from DBCLS SRA