DAC University of Cologne

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Graziella Bosco
gbosco@uni-koeln.de

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This DAC controls 24 datasets

Dataset ID	Description	Technology	Samples
EGAD00001000703	SCLC - Whole genome sequencing data Publication Peifer et al., 2012, Nature Genetics	Illumina Genome Analyzer IIx	29
EGAD00001000716	RNAseq data, Publication Fernandez-Cuesta et al., 2014, CD74-NRG1 fusions in lung adenocarcinoma	Illumina HiSeq 2000	25
EGAD00001000746	Fernandez-Cuesta et al., RNAseq data Pipline	Illumina HiSeq 2000	25
EGAD00001000795	Fernandez-Cuesta et al, 2014, Nature Communication, RNA Sequencing data set	Illumina HiSeq 2000	69
EGAD00001000813	Fernandez-Cuesta et al., 2014, Nature Communication, Whole genome sequencing was performed using a read length of 2x100 bp for all samples. On average, 110 Gb of sequence were produced per sample, aiming a mean coverage of 30x for both tumour and matched normal.	Illumina HiSeq 2000	29
EGAD00001000820	Fernandez-Cuesta et al, 2014, Nature Communication, Whole exome sequencing data set	Illumina HiSeq 2000	15
EGAD00001000977	WGS dataset LCNEC study	Illumina HiSeq 2000	11
EGAD00001001244	RNA-sequencing (RNA-seq) was performed with RNA extracted from fresh-frozen human tumor tissue samples. cDNA libraries were prepared from poly-A selected RNA applying the Illumina TruSeq protocol for mRNA. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x of the annotated transcriptome.	Illumina HiSeq 2000	59
EGAD00001001273	Whole genome sequencing was performed with DNA extracted from fresh-frozen tumor and normal material. Short insert DNA libraries were prepared with the TruSeq DNA PCRfree sample preparation kit (Illumina) for paired-end sequencing at a minimum read length of 2x100bp. Human DNA libraries were sequenced to an average coverage of minimum 30x for both tumor and matched normal. Murine DNA libraries of tumor and matched normal were both sequenced to a coverage of 25x.	Illumina HiSeq 2000	100
EGAD00001001431	SCLC - RNA sequencing data Publication Peifer et al., 2012, Nature Genetics	Illumina HiSeq 2000	15
EGAD00001003099	RNAseq data set (Mollaoglu et al., MYC drives progression of small cell lung cancer to a variant neuroendocrine subtype with vulnerability to Aurora kinase inhibition) RNA isolation from primary tumors and healthy lungs was performed using RNeasy Mini Kit (Qiagen) with the standard protocol. RNA was subjected to library construction with the Illumina TruSeq Stranded mRNA Sample Preparation Kit (cat# RS-122-2101, RS-122-2102) according to manufacturer’s protocol. Chemically denatured sequencing libraries (25 pM) are applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001). Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).	Illumina HiSeq 2000	14
EGAD00001003316	RNAseq of LC2AD with AD80 or DMSO Plenker et al., Mechanistic insight into RET kinase inhibitors targeting the DFG-out conformation in RET-rearranged cancer	Illumina HiSeq 2000	1
EGAD00001003464	For RNA-Seq total RNA was isolated following LDC67 or JQ1 treatment. 3’RNAseq libraries were prepared with QUANT SEQ FWD 3´mRNA-Seq Kit (Lexogen, Austria), sequenced on an Illumina HiSeq 4000	Illumina HiSeq 2000	3
EGAD00001003801	RNAseq Data set	Illumina HiSeq 2000	40
EGAD00001003815	Whole exome sequencing	Illumina HiSeq 2000	48
EGAD00001003969	RNA-seq analyses were performed on cDNA libraries prepared from PolyA+ RNA using the Illumina TruSeq protocol for mRNA. The final libraries were sequenced with a paired-end 2×75 bp protocol aiming at 8.5 Gb per sample for a 30x mean coverage of the annotated transcriptome. All sequencing reactions were conducted on an Illumina HiSeq instrument (Illumina, San Diego, CA, USA).	Illumina HiSeq 2000	7
EGAD00001003970	For whole-exome sequencing 1 µg of DNA from fresh-frozen tumors was fragmented by sonication technology (for DNA from fresh-frozen tumors: Bioruptor, diagenode, Liѐge, Belgium; for DNA from FFPE material: Covaris). The fragments were end-repaired and adaptor-ligated, including incorporation of sample index barcodes. After size selection, libraries were subjected to an enrichment process with Sure select XT (Agilent). The final libraries were sequenced with a paired-end 2×75 bp protocol for an average coverage of 100-120x	Illumina HiSeq 2000	7
EGAD00010000526	SNP 6.0 arrays of small cell lung cancer	Affymetrics_SNP_6.0-	63
EGAD00010000546	SNP 6.0 arrays of carcinoid samples	Affymetrics_SNP_6.0-	74
EGAD00010000554	SNP 6.0 arrays of small cell lung cancer		1032
EGAD00010000556	SNP 6.0 arrays of small cell lung cancer		1
EGAD00010000558	SNP 6.0 arrays of small cell lung cancer	Affymetrix SNP 6.0	54
EGAD00010001511	SNP 6.0 arrays of LCNEC samples	Affymetrix SNP 6.0	54
EGAD50000000243	We performed whole exome sequencing, whole genome sequencing and transcriptome sequencing of multiple tumor regions from 65 patients with SCLC.	unspecified	423