Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PML

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
GSM1010838
antibody antibodydescription
Mouse monoclonal IgG, N-terminal epitope corresponding to residues 37-51 of PML of human origin. Antibody Target: PML
antibody targetdescription
The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq)
antibody vendorid
sc-71910
antibody vendorname
Santa Cruz Biotechnology
antibody
PML_(SC-71910)
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,SL16756
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL16026,SL13722
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
GSM1010838: HudsonAlpha_ChipSeq_MCF-7_PML_(SC-71910)_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
69890962
Reads aligned (%)
81.4
Duplicates removed (%)
9.1
Number of peaks
13694 (qval < 1E-05)

hg38

Number of total reads
69890962
Reads aligned (%)
82.9
Duplicates removed (%)
8.0
Number of peaks
13834 (qval < 1E-05)

Base call quality data from DBCLS SRA