Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
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.)
controlid
SL2905
labexpid
SL2905
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
RevXlinkChromatin
treatment
None
treatment description
No special treatment or protocol applies
protocol
v041610.2
protocol description
2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)
controlid
SL2905
labexpid
SL2905
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803526: HudsonAlpha_ChipSeq_SK-N-SH_RA_RevXlinkChromatin_v041610.2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
29299375
Reads aligned (%)
95.2
Duplicates removed (%)
3.8
Number of peaks
612 (qval < 1E-05)

hg19

Number of total reads
29299375
Reads aligned (%)
94.4
Duplicates removed (%)
4.5
Number of peaks
861 (qval < 1E-05)

Base call quality data from DBCLS SRA