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
cell type
Control
chip antibody
H3K4me3; Millipore, #04-745

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Genomic DNA were extracted using antibodies for EPOP, H3K4me3, Elongin B, RNA Polymerase II S5, USP7 or H2Bub. RNA-Seq samples were prepared by isolating total RNA using Trizol, mRNA Isolation, heat fractionation, reverse transcription and second strand synthesis Libraries were constructed of 10-50 ng of DNA following Illumina's® protocol

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
25936911
Reads aligned (%)
97.5
Duplicates removed (%)
33.0
Number of peaks
22590 (qval < 1E-05)

hg19

Number of total reads
25936911
Reads aligned (%)
97.3
Duplicates removed (%)
33.1
Number of peaks
22466 (qval < 1E-05)

Base call quality data from DBCLS SRA