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
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
controlid
SL1714
labexpid
SL1714
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
RevXlinkChromatin
treatment
None
treatment description
No special treatment or protocol applies
protocol
v041610.1
protocol description
2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)
controlid
SL1714
labexpid
SL1714
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803423: HudsonAlpha_ChipSeq_SK-N-MC_RevXlinkChromatin_v041610.1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
43655784
Reads aligned (%)
87.5
Duplicates removed (%)
1.4
Number of peaks
734 (qval < 1E-05)

hg19

Number of total reads
43655784
Reads aligned (%)
86.9
Duplicates removed (%)
2.4
Number of peaks
1095 (qval < 1E-05)

Base call quality data from DBCLS SRA