Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
SK-N-MC
Primary Tissue
Brain
Site of Extraction
Brain
Tissue Diagnosis
neuroepithelioma

Attributes by original data submitter

Sample

source_name
SK-N-MC
biomaterial_provider
ATCC
lab
UW
lab description
Stamatoyannopoulous - University of Washington
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
SK-N-MC
cell organism
human
cell description
neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (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
Input
antibody description
Control signal which may be subtracted from experimental raw signal before peaks are called.
treatment
None
treatment description
No special treatment or protocol applies
control
std
control description
Standard input signal for most experiments.
controlid
wgEncodeEH001901
labexpid
DS18341
labversion
WindowDensity-bin20-win+/-75
replicate
1

Sequenced DNA Library

library_name
GSM1022638: UW_ChipSeq_SK-N-MC_InputRep1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
21786302
Reads aligned (%)
99.1
Duplicates removed (%)
3.5
Number of peaks
559 (qval < 1E-05)

hg19

Number of total reads
21786302
Reads aligned (%)
98.2
Duplicates removed (%)
5.1
Number of peaks
878 (qval < 1E-05)

Base call quality data from DBCLS SRA