Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of epithelial and mesenchymal populations in tumor-derived cell lines by scRNA-seq

ABSTRACT: This experiment includes single cell transcriptome data for the epithelial and mesenchymal populations isolated from a pancreatic tumor induced in GEM mouse.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Davide Cittaro

PROVIDER: E-MTAB-13051 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Analysis of epithelial and mesenchymal populations in tumor-derived cell lines by scGET-seq

Project description:This experiment includes single cell epigenome data (by scGET-seq) for the epithelial and mesenchymal populations isolated from a pancreatic tumor induced in GEM mouse.

2024-06-01 | E-MTAB-13052 | biostudies-arrayexpress

Single cell RNA-seq analysis of cancer cell lines upon administration of FOLFOX or FOLFIRI at different time points

Project description:This experiment is aimed at studying the effect of two different chemotherapies (FOLFOX and FOLFIRI) on colorectal cancer cell lines (HCT116 and HT29) at different time points. Two early time points (8h and 16h) are used to evaluate the acute response, while a late time point (two weeks, LT) is used to evaluate the long-term effect. After two week exposure, cells are grown without treatments for additional two weeks, to evaluate the transcriptomic of cells which survived the chemotherapy. A pool of the same cells has been independently profiled by scGET-seq.

2023-09-01 | E-MTAB-12949 | biostudies-arrayexpress

Single cell RNA-seq analysis of cancer cell lines upon administration of FOLFOX or FOLFIRI at different time points

Project description:This experiment is aimed at studying the effect of two different chemotherapies (FOLFOX and FOLFIRI) on gene expression of HCT116 colorectal cancer cell line at different time points. Two early time points (8h and 16h) are used to evaluate the acute response, while a late time point (two weeks, LT) is used to evaluate the long-term effect. After two week exposure, cells are grown without treatments for additional two weeks, to evaluate the transcriptomic of cells which survived the chemotherapy. For all time points, untreated cells (CTRL) are also collected.

2023-09-01 | E-MTAB-12950 | biostudies-arrayexpress

Epigenetic profile of iPSC differentiation process by scRNA-seq

Project description:Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scRNA-seq.

2021-08-17 | E-MTAB-10220 | biostudies-arrayexpress

Single cell RNA-seq profiles of patient derived organoids

Project description:Three patient-derived organoids from liver metastasis of CRC samples were profiled by scRNA-seq.

2024-02-29 | E-MTAB-13123 | biostudies-arrayexpress

Single cell tracking of expressed barcodes in cancer cell lines upon administration of FOLFOX or FOLFIRI at different time points

Project description:This experiment is aimed at studying the effect of two different chemotherapies (FOLFOX and FOLFIRI) on HCT116 colorectal cancer cell line on clonal heterogeneity. One early time point (8h) is used to evaluate the initial population, while a late time point (two weeks, LT) is used to evaluate the long-term effect. After two week exposure, cells are grown without treatments for additional two weeks.

2023-09-01 | E-MTAB-12951 | biostudies-arrayexpress

scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress

Cellular plasticity and diversity during heart valve epithelial-to-mesenchymal transitions revealed using single-cell RNA-seq

Project description:We have generated scRNA-seq data from embryonic day (E)10.5 and E12.5 atrioventricular canals (primitive heart valves) to assess cellular diversity during the distinct epithelial-to-mesenchymal transitions (EMTs) from endocardium and epicardium that guide the formation of valve mesenchyme. Alongside, wildtype atrioventricular canals, we generated scRNA-seq data from Sox9 conditional knockouts (Sox9fl/fl;Tie2-cre) to explore the role of SOX9 in EMT. Atrioventricular canals were microdissected from cardiac chambers and outflow tract, enriching for heart valve progenitor lineages.

2023-06-30 | E-MTAB-11795 | biostudies-arrayexpress

Timecourse single-cell RNAseq of whole mouse embryos harvested between days 6.5 and 8.5 of development.

Project description:We have captured 100,000 single cells for single-cell RNAseq from whole mouse embryos during gastrulation and organogenesis, spanning days 6.5 to 8.5 of development, including embryonic and extraembryonic tissues. Cells were sampled every six hours, providing a continuous molecular characterisation of these processes. Cell libraries were prepared using the 10X Genomics Chromium platform.

2018-12-05 | E-MTAB-6967 | biostudies-arrayexpress

Single-cell RNAseq of whole B6 mouse E8.25 embryos

Project description:Gastrulation represents a pivotal point in mammalian development, when the basic body plan is established and cells are specified into one of the three germ layers. This is followed by rapid diversification into specific lineages and the appearance of the various cell types required to build each of the organs. The rich variety of cell types present at this stage has never been rigorously characterised in any mammalian organism, and thus insight into cell fate decisions and the underlying regulatory networks have been inaccessible. We have used droplet based single-cell RNA-sequencing to address this by profiling ~20000 cells from C57BL/6 E8.25 mouse embryos.

2017-12-01 | E-MTAB-6153 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data