Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PGBD5

Cell type

Cell type Class
Kidney
Cell type
Rhabdoid Tumor
MeSH Description
A rare but highly lethal childhood tumor found almost exclusively in infants. Histopathologically, it resembles RHABDOMYOSARCOMA but the tumor cells are not of myogenic origin. Although it arises primarily in the kidney, it may be found in other parts of the body. The rhabdoid cytomorphology is believed to be the expression of a very primitive malignant cell. (From Holland et al., Cancer Medicine, 3d ed, p2210)

Attributes by original data submitter

Sample

source_name
kidney
tumor type
rhabdoid tumor
tissue
kidney
chip antibody
Rabbit anti-PGBD5, orb13159,Biorbyt, Berkeley, CA, USA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Extraction protocol not provided, ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
20811241
Reads aligned (%)
181.6
Duplicates removed (%)
6.5
Number of peaks
301 (qval < 1E-05)

hg38

Number of total reads
20811241
Reads aligned (%)
183.0
Duplicates removed (%)
6.4
Number of peaks
407 (qval < 1E-05)

Base call quality data from DBCLS SRA