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TranscriptomicsSingle-cell RNA-seq of Ecad positive PyMT bulk tumor cells
In this study we studied the presence of tumor cells that underwent epithelial-to-mesenchymal transition within polyoma middle T antigen (PyMT) breast tumors. For this we dissociated tumors and isolated Ecad positive tumor cells by FACS sorting. We confirmed that PyMT tumors contain a small set of t...
ORGANISM(S): Mus musculus 
2016-03-09 | E-GEOD-77107 | biostudies-arrayexpress
GenomicsIntegrated genome and transcriptome sequencing from the same cell
Single-cell genomics and single-cell transcriptomics have recently emerged as powerful tools to study the biology of single cells at a genome-wide scale. Here we describe a method that allows the integration of genomic DNA and mRNA sequencing from the same cell. We use this method to correlate DNA c...
ORGANISM(S): Mus musculus 
2014-12-11 | E-GEOD-62952 | biostudies-arrayexpress
TranscriptomicsValidation of noise models for single-cell transcriptomics
Single-cell transcriptomics has recently emerged as a powerful technology to explore gene expression heterogeneity amongst single cells. Here we identify two major sources of technical variability, sampling noise and global cell-to-cell variation in sequencing efficiency. We propose noise models to ...
ORGANISM(S): Mus musculus 
2014-04-20 | E-GEOD-54695 | biostudies-arrayexpress
TranscriptomicsProspective derivation of a 'Living Organoid Biobank' of colorectal cancer patients
In Rspondin-based three-dimensional cultures, Lgr5 stem cells from multiple organs form ever-expanding epithelial organoids that retain their tissue identity. Here we report the establishment of tumor organoid cultures from 20 consecutive colorectal carcinoma (CRC) patients. For most, organoids were...
ORGANISM(S): Homo sapiens 
2015-05-07 | E-GEOD-65253 | biostudies-arrayexpress
Genomicsena-DATASET-UMCU-04-11-2019-12:52:17:220-46 - samples
WGS Nanopore nanopore sequencing of organoid line HGS-3.1 and matching blood reference HGS-3
EGAD00001005476 | EGA
Genomicsena-DATASET-UMCU-10-10-2018-09:56:24:582-1061 - samples
WGS of ovarian cancer organoids, tumor samples and blood references. Ovarian cancer (OC) is a heterogeneous disease usually diagnosed at a late stage. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of OC are limited and hard to establish. We present a nove...
EGAD00001004387 | EGA
Genomicsena-DATASET-UMCU-12-12-2018-15:19:19:893-122 - samples
Ovarian cancer (OC) is a heterogeneous disease usually diagnosed at a late stage. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of OC are limited and hard to establish. We present a novel protocol that enables efficient derivation and long-term expansion ...
EGAD00001004509 | EGA
Genomicsena-DATASET-UMCU-29-11-2019-11:40:53:733-901 - samples
WGS of more samples in the ovarian cancer organoid biobank dataset.
EGAD00001005707 | EGA
GenomicsOvarian cancer organoid biobank
Ovarian cancer (OC) is a heterogeneous disease usually diagnosed at a late stage. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of OC are limited and hard to establish. We present a novel protocol that enables efficient derivation and long-term expansion ...
EGAS00001003073 | EGA
TranscriptomicsCell-autonomous transformation of Lgr5-positive intestinal stem cells into gastric stem cells upon loss of transcription factor Cdx2
Stomach and intestinal adult epithelia harbor stem cells that are responsible for their continuous regeneration. Stomach and intestinal stem cells differ in their differentiation program and in the gene repertoire that they express. We show that single adult Lgr5-positive stem cells, isolated from 3...
ORGANISM(S): Mus musculus 
2014-12-05 | E-GEOD-62784 | biostudies-arrayexpress
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