Antigen

Antigen Class

DNase-seq

Antigen

DNase-Seq

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).

Sample

DISEASE_ONTOLOGY_URI

C2853894

ENA first public

2014-08-12

ENA last update

2018-03-08

ENA-CHECKLIST

ERC000011

External Id

SAMEA2165297

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

2018-03-08T16:39:00Z

INSDC status

public

SAMPLE_ONTOLOGY_URI

http://www.ebi.ac.uk/efo/EFO_0005479

Submitter Id

Z-138_d01

biomaterial provider

WP4_Bergmann_Siebert_Martin-Subero

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

Z-138

medium

RPMI 1640 + 10%FBS

molecule

genomic DNA

sample name

Z-138_d01

sex

male

Sequenced DNA Library

library_name

blueprintWP4_Z138_DNaseI_60U_18M_starting cells

library_strategy

DNase-Hypersensitivity

library_source

GENOMIC

library_selection

DNase

library_construction_protocol

Z138 cell line nuclei were isolated and briefly treated with different concentrations of DNaseI enzyme. Based on quality check 60U DNase treated sample was further processed with sucrose fractionation and purified sample was passed to the illumina library

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

65474265

Reads aligned (%)

94.6

Duplicates removed (%)

16.3

Number of peaks

65036 (qval < 1E-05)

hg19

Number of total reads

65474265

Reads aligned (%)

93.6

Duplicates removed (%)

18.2

Number of peaks

66306 (qval < 1E-05)