Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SIN3A

Cell type

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

Attributes by original data submitter

Sample

GEO Accession
GSM1010816
antibody antibodydescription
Rabbit polyclonal, Sin3A (k-20). Antibody Target: SIN3AK20
antibody targetdescription
Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2
antibody vendorid
sc-994
antibody vendorname
Santa Cruz Biotechnology
antibody
Sin3Ak-20
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.
cell karyotype
cancer
cell lineage
ectoderm
cell organism
human
cell sex
F
cell
SK-N-SH
controlid
SL3774,SL3775
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL5895,SL5043
protocol description
2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)
protocol
v041610.1
replicate
1,2
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010816: HudsonAlpha_ChipSeq_SK-N-SH_Sin3Ak-20_v041610.1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
77713691
Reads aligned (%)
56.0
Duplicates removed (%)
30.0
Number of peaks
22190 (qval < 1E-05)

hg38

Number of total reads
77713691
Reads aligned (%)
57.1
Duplicates removed (%)
29.1
Number of peaks
22292 (qval < 1E-05)

Base call quality data from DBCLS SRA