Multi-omic dataset of neuroendocrine neoplasm organoids - EGA European Genome-Phenome Archive

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001009988	The dataset includes cram files from WGS of 2 NEN tumors and matched PDTOs. For all tumors, cram files from WGS of matched normal tissue from the corresponding patients are included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.	Illumina NovaSeq 6000	1
EGAD00001009989	The dataset includes cram files from WGS of 6 NEN tumors or metastases and matched PDTOs. For all tumors, cram files from WGS of either matched normal tissue or matched blood from the corresponding patients are included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.	Illumina NovaSeq 6000	1
EGAD00001009990	The dataset includes cram files from WGS of 2 LCNEC tumors and matched PDTOs. For all tumors, cram files from WGS of matched normal tissue derived organoids from the corresponding patients is included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.	Illumina NovaSeq 6000	1
EGAD00001009991	The dataset includes fastq files from 4 NEN tumors or metastases and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.	Illumina NovaSeq 6000	1
EGAD00001009992	The dataset includes fastq files from 15 NEN tumors or metastases and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.	Illumina NovaSeq 6000 NextSeq 500	1
EGAD00001009993	The dataset includes fastq files from 2 LCNEC tumors and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.	Illumina NovaSeq 6000 NextSeq 500	1
EGAD00001009994	The dataset includes RNA-seq expression R data, RNA-seq gene counts matrix, and RNA-seq gene FPKM matrix from 21 NEN tumors or metastases and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.		1

Publications	Citations
Multi-omic dataset of patient-derived tumor organoids of neuroendocrine neoplasms. Alcala N, Voegele C, Mangiante L, Sexton-Oates A, Clevers H, Fernandez-Cuesta L, Dayton TL, Foll M. Gigascience 13: 2024 giae008	1