Comment[ArrayExpressAccession]	E-MTAB-7722
MAGE-TAB Version	1.1
Comment[Submitted Name]	The LL-100 panel: 100 DSMZ cell lines for blood cancer studies; WES
Investigation Title	The LL-100 panel: 100 DSMZ cell lines for blood cancer studies; WES
Experiment Description	For many years, immortalized cell lines have been used as model systems for cancer research. Cell line panels were established for basic research and drug development, but did not cover the full spectrum of leukemia and lymphoma. Therefore, we now developed a novel panel (LL-100), 100 cell lines covering 22 entities of human leukemia and lymphoma including T-cell, B-cell and myeloid malignancies. Importantly, all cell lines are unequivocally authenticated and assigned to the correct tissue. Cell line samples were proven to be free of mycoplasma and virus contamination. Whole exome sequencing (WES) and RNA sequencing (RNA-seq) of the hundred authenticated leukemia-lymphoma cell lines were conducted with a uniform methodology to complement existing data on these publicly available cell lines. This part captures WES. This data set will be useful for understanding the function of oncogenes and tumor suppressor genes and to develop targeted therapies.
Experimental Design	cell type comparison design	disease state design
Experimental Design Term Source REF	EFO	EFO
Experimental Design Term Accession Number	EFO:0001745	EFO:0001756
Experimental Factor Name	cell type	disease
Experimental Factor Type	cell type	disease
Experimental Factor Term Source REF	EFO	EFO
Experimental Factor Term Accession Number	EFO_0000324	EFO_0000408
Person Last Name	Pommerenke
Person First Name	Claudia
Person Mid Initials
Person Email	claudia.pommerenke@dsmz.de
Person Phone
Person Fax
Person Address	Inhoffenstraße 7B 38124 Braunschweig
Person Affiliation	Leibniz Institute DSMZ
Person Roles	submitter
Public Release Date	2019-05-28
Protocol Name	P-MTAB-83383	P-MTAB-83384	P-MTAB-83385	P-MTAB-83386
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO
Protocol Term Accession Number	EFO_0005518	EFO_0002944	EFO_0004184	EFO_0004170
Protocol Description	Cell lines were taken from the stock of the cell lines bank (Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures). Cell lines were authenticated by DNA profiling and cytogenetics.	DNA was isolated with the High Pure PCR Template Preparation Kit (Roche Diagnostics, Mannheim, Germany).	Library preparation (Agilent SureSelect Human All Exon V6, 60MB) and sequencing steps (2x151 bp + 8 bp barcoding, HiSeqX) were commissioned to Genewiz (Leipzig, Germany)	2x151 bp + 8 bp barcoding, HiSeqX
Protocol Hardware				HiSeq X Ten
Protocol Software
Term Source Name	EFO
Term Source File	http://www.ebi.ac.uk/efo/
Term Source Version
Comment[TemplateType]	Cell line - High-throughput sequencing
Comment[AEExperimentType]	DNA-seq
Comment[RelatedExperiment]	E-MTAB-7721
Comment[SecondaryAccession]	ERP112730
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR2990053-ERR2990152
SDRF File	E-MTAB-7722.sdrf.txt
PubMed ID
Publication DOI
Publication Author List	Quentmeier H, Pommerenke C, Dirks WG, Eberth S, Koeppel M, MacLeod RAF, Nagel S, Steube K, Uphoff CC, Drexler HG.
Publication Title	The LL-100 panel: 100 cell lines for blood cancer studies.