Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Neural
Cell type
SK-N-FI
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
neuroblastoma-derived cell line
growth media
RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine
cell line
SK-N-FI
chip antibody
H3K4me1 (Active Motif, #39297)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, cells were crosslinked, flash frozen, and sent to Active Motif. According to Active Motif protocol, cells were lysed, sonicated, and then DNA-protein complexes were isolated with antibodies. Samples were reverse-crosslinked and DNA was purified. For ATAC-Seq, whole cells were frozen and sent to Active Motif for thawing and transposition. Illumina libraries were prepared by Active Motif using standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After 15 cycles of PCR amplification, the resulting DNA libraries were quantified and sequenced by Jefferson Cancer Genomics Laboratory at the Kimmel Cancer Center using the NexSeq 500.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
52525768
Reads aligned (%)
98.4
Duplicates removed (%)
6.6
Number of peaks
54079 (qval < 1E-05)

hg19

Number of total reads
52525768
Reads aligned (%)
98.1
Duplicates removed (%)
7.0
Number of peaks
53804 (qval < 1E-05)

Base call quality data from DBCLS SRA