SRX100573
GSM803528: HudsonAlpha ChipSeq SK-N-SH RevXlinkChromatin PCR2x

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
biomaterial_provider
ATCC
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.
protocol description
a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)
controlid
SL108,SL410
labexpid
SL108,SL410
replicate
1,2
cell karyotype
cancer
cell lineage
ectoderm
cell sex
F
antibody
RevXlinkChromatin
treatment
None
treatment description
No special treatment or protocol applies
protocol
PCR2x
protocol description
2-cycles of PCR (Myers)
controlid
SL108
labexpid
SL108
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803528: HudsonAlpha_ChipSeq_SK-N-SH_RevXlinkChromatin_PCR2x
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
67799235
Reads aligned (%)
48.5
Duplicates removed (%)
7.3
Number of peaks
17669 (qval < 1E-05)

hg19

Number of total reads
67799235
Reads aligned (%)
48.2
Duplicates removed (%)
7.6
Number of peaks
17608 (qval < 1E-05)

Base call quality data from DBCLS SRA