Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

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

Attributes by original data submitter

Sample

source_name
SK-N-SH_RA
biomaterial_provider
ATCC
lab
UW
lab description
Stamatoyannopoulous - University of Washington
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
SK-N-SH_RA
cell organism
human
cell description
neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)
cell karyotype
cancer
cell lineage
ectoderm
cell sex
F
antibody
H3K4me3
antibody antibodydescription
rabbit polyclonal. Antibody Target: H3K4me3
antibody targetdescription
Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
antibody vendorname
Millipore
antibody vendorid
07-473
treatment
None
treatment description
No special treatment or protocol applies
control
std
control description
Standard input signal for most experiments.
controlid
wgEncodeEH000474
labexpid
DS11782
labversion
Bowtie 0.12.5
replicate
1

Sequenced DNA Library

library_name
GSM945202: UW_ChipSeq_SK-N-SH_RA_H3K4me3
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
34386635
Reads aligned (%)
93.5
Duplicates removed (%)
26.2
Number of peaks
32151 (qval < 1E-05)

hg19

Number of total reads
34386635
Reads aligned (%)
93.3
Duplicates removed (%)
26.5
Number of peaks
32156 (qval < 1E-05)

Base call quality data from DBCLS SRA