Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Blood
Cell type
Lymphoma, Mantle-Cell
MeSH Description
A form of non-Hodgkin lymphoma having a usually diffuse pattern with both small and medium lymphocytes and small cleaved cells. It accounts for about 5% of adult non-Hodgkin lymphomas in the United States and Europe. The majority of mantle-cell lymphomas are associated with a t(11;14) translocation resulting in overexpression of the CYCLIN D1 gene (GENES, BCL-1).

Attributes by original data submitter

Sample

DISEASE_ONTOLOGY_URI
C0334634
ENA first public
2014-08-12
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2165289
INSDC center alias
NCMLS
INSDC center name
Nijmegen Centre for Molecular Life Sciences - Radboud University
INSDC first public
2014-08-12T17:01:04Z
INSDC last update
2018-03-08T16:38:13Z
INSDC status
public
SAMPLE_ONTOLOGY_URI
http://purl.obolibrary.org/obo/CLO_0007047
Submitter Id
JVM-2_c01
biomaterial provider
DSMZ
biomaterial type
Cell Line
common name
human
differentiation method
Drexler HG chapter 16 Establishment and culture of leukemia-lymphoma cell in Cancer Cell Culture Methods and Protocols 2nd Edition Springer Berlin pp 181 to 200 in 2011
differentiation stage
B cell
disease
Mantle Cell Lymphoma
line
JVM-2
medium
RPMI 1640 + 10%FBS
molecule
genomic DNA
sample name
JVM-2_c01
sex
female

Sequenced DNA Library

library_name
blueprint_JVM2_H3K4me3
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
NEXTflex ChIP-Seq from Bioo Scientific, 10 cycle PCR at the end and last purification is performed with magnetic beads.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
44043413
Reads aligned (%)
98.5
Duplicates removed (%)
20.9
Number of peaks
48683 (qval < 1E-05)

hg19

Number of total reads
44043413
Reads aligned (%)
98.2
Duplicates removed (%)
21.1
Number of peaks
50185 (qval < 1E-05)

Base call quality data from DBCLS SRA