Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Neural
Cell type
SH-SY5Y
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
SH-SY5Y_siCTL_K4me3_ChIP-seq
cell line
SH-SY5Y
cell type
neuronal cell line
sirna
siCTL
genotype/variation
control knockdown
chip antibody
H3K4me3 (Active Motif 39159, LOT#GR288375-1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
WGBS: Illumina TruSeq DNA Methylation Kit (Illumina EGMK81312) RNA-seq: NEB NEBNext rRNA Depletion Kit (NEB E6310L) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB E7420S) ChIP-seq: KAPA Hyper Prep Kit (Kapa KK8504)

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
40582841
Reads aligned (%)
99.2
Duplicates removed (%)
21.9
Number of peaks
598 (qval < 1E-05)

hg19

Number of total reads
40582841
Reads aligned (%)
98.8
Duplicates removed (%)
22.4
Number of peaks
756 (qval < 1E-05)

Base call quality data from DBCLS SRA