Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SIN3A

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

GEO Accession
GSM1010862
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
mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis
cell karyotype
cancer
cell lineage
ectoderm
cell organism
human
cell sex
F
cell
MCF-7
controlid
SL16757,SL13504
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL14716,SL13726
protocol description
Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)
protocol
v042211.1
replicate
1,2
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010862: HudsonAlpha_ChipSeq_MCF-7_Sin3Ak-20_v042211.1
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
74569593
Reads aligned (%)
76.5
Duplicates removed (%)
14.1
Number of peaks
43474 (qval < 1E-05)

hg38

Number of total reads
74569593
Reads aligned (%)
78.1
Duplicates removed (%)
12.9
Number of peaks
43761 (qval < 1E-05)

Base call quality data from DBCLS SRA