Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Neural
Cell type
Neuroblatoma cell lines
NA
NA

Attributes by original data submitter

Sample

source_name
Neuroblatoma TIC line
cell type
Neuroblatoma TIC line
growth medium
neural stem cell medium
chip antibody
H3K4me3 (#04-745, Millipore)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cultured cells were fixed with 1% formaldehyde. Nuclei were isolated and the DNA was sheared to 200 to 300 bp fragments. Histon-bound DNA was precipitated using antibodies H3K27Ac (#4729, Abcam) and H3K4me3 (#04-745, Millipore). De-crosslinked DNA was purified using Qiagen PCR purification kit (Qiagen) and quantified with Quant-IT Picogreen (Invitrogen). The DNA was used to generate sequencing libraries according to the manufactures procedure (Life Technologies): The DNA was end-polished, dA-tailed and adaptors with barcodes were ligated. The fragments were amplified (8 cycles) and quantified with a Bioanalyzer (Agilent). The libraries were prepped with the 5500W Flowchip v2 kit (Life Technologies) and sequenced on the SOLiD Wildfire (Illumina) resulting in 50 bp reads. Alternatively, the libraries were sequenced using the HiSeq PE cluster kit v4 (Illumina) with the HiSeq2500 (Illumina) resulting in 125 bp reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
36662560
Reads aligned (%)
98.2
Duplicates removed (%)
17.2
Number of peaks
28993 (qval < 1E-05)

hg19

Number of total reads
36662560
Reads aligned (%)
100.0
Duplicates removed (%)
17.6
Number of peaks
27164 (qval < 1E-05)

Base call quality data from DBCLS SRA