Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-seq of human kidney tumors

ABSTRACT: The current dataset contains the transcriptomic information of fresh single cells originating from human clear cell renal cell carcinomas (ccRCC). Samples have been experimentally enriched in malignant cells in order to address specific questions regarding heterogeneity and clonality in ccRCC. Samples include one set of long-term frozen and thawed single cells in order to explore the impact of liquid nitrogen freezing on ccRCC single cells.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Judikael Saout

PROVIDER: E-MTAB-11310 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

An integrated approach to profile lung tumor endothelial cell heterogeneity across species and models and to identify angiogenic candidates

Project description:Heterogeneity of lung tumor endothelial cell (TEC) phenotypes across patients, species (human/mouse) and models (in vivo/vitro) remains poorly inventoried at the single-cell-level. We single-cell RNA-sequenced 56,771 ECs from human/mouse (peri)-tumoral lung and cultured human lung TECs, detected 17 known and discovered 16 novel phenotypes, including TECs presumably regulating immune surveillance. We resolved the canonical tip TECs into a known migratory tip and a novel basement-membrane remodeling breach phenotype. Tip-TEC signatures correlated with patient-survival, and tip/breach TECs were most sensitive to VEGF-blockade. By similarity analysis, only tip-TECs were congruent across species/models and shared conserved markers. Integrated analysis of the scRNA-seq data with orthogonal multi-omics and meta-analysis data across different human tumors, validated by functional analysis, identified collagen-modification as angiogenic candidate pathway.

2019-12-30 | E-MTAB-6308 | biostudies-arrayexpress

An integrated approach to profile lung tumor endothelial cell heterogeneity across species and models and to identify angiogenic candidates

2020-05-20 | E-MTAB-7458 | biostudies-arrayexpress

Boundary caps: a major source of skin mural cells

Project description:In the study we show that a specific peripheral glial population, derived from boundary cap (BC) cells, constitutes a major source of mural cells for the developing vasculature. Using Cre-based reporter cell tracing and single cell transcriptomics, we show that BC cell derivatives migrate along the nerves and differentiate into pericytes and vascular smooth muscle cells in the skin. The switch from glial to mural molecular identity is initiated while the cells are still associated with nerves To further characterize this transition glial to vascular identity, we performed single cell transcriptomic analyses (scRNA-seq) on FACS-purified traced cells from dissociated E12.5 skin. Tomato-positive cells were isolated by FACS from embryonic skin at E12.5. Around 10,000 cells were loaded into one channel of the Chromium system using the V3 single cell reagent kit (10X Genomics) We analyzed 2527 single cell transcriptomes with a mean number of expressed genes per cell of 4,696. This study highlights the plasticity of BC derivatives and uncovers a novel, nerve-derived origin for skin mural cells.

2023-11-30 | E-MTAB-8972 | 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

microRNAseq of clear-cell renal cell carcinoma on surgical resection specimens of untreated primary tumors in humans

Project description:We aimed to assess differences in miRNA expression profiles in transcriptomic molecular subtypes of ccRCC (Beuselinck et al, Clinical Cancer Research 2015) and to correlate miRNAs with overal survival since diagnosis of ccRCC. Sequencing was done for 129 primary ccRCC (formalin-fixed paraffin-embedded surgical resection specimens, previously untreated) and 16 normal kidney specimens. Normal kidney was obtained from the nephrectomy specimens at time of ccRCC removal, in tissue blocks containing only normal kidney (so nót the normal kidney immediately adjacent to ccRCC). The samples were sequenced in 2 major batches (2014 and 2017).

2020-07-22 | E-MTAB-9380 | biostudies-arrayexpress

scRNA-seq of Multi-lineage differentiating Stress Enduring (Muse) cell and non-Muse cells isolated from bone marrow-derived mesenchymal stem cells

Project description:MSCs comprise several percent of pluripotent-like cells named Multilineage-differentiating stress enduring (Muse) cells that express pluripotent markers at moderate levels, are collectable as cells positive for the pluripotent surface marker SSEA-3, are able to differentiate into triploblastic lineage cells, and self-renew at the single cell level (Kuroda et al, PNAS, 2010; Wakao et al, PNAS, 2011). Importantly, MSCs also comprise cells other than SSEA-3(+)-Muse cells, namely multipotent SSEA-3(-)-non-Muse MSCs that correspond to ~98% of the total MSC population. These SSEA-3(-)-non-Muse MSCs exhibit the same properties as conventional MSCs, although the non-Muse MSCs are multipotent, they are not pluripotent. In the present study, to clarify the key molecules that characterize pluripotent-like vs multipotent somatic stem cells, we separated human MSCs into SSEA-3(+)-Muse cells and SSEA-3(-)-non Muse MSCs, and analyzed both populations by scRNA-seq. SSEA-3(+) Muse cells and SSEA-3(-) non-Muse MSCs were sorted from human BM-MSCs. Sequencing libraries were prepared using Chromium single cell 3' Kit v3 (10x Genomics, Pleasanton, CA, USA) and sequenced on HiSeq2500 (Illumina, San Diego, CA, USA). Transcripts were mapped with CellRanger pipeline v3 (10x Genomics). Library construction, sequencing, and initial analysis were performed by GENEWIZ (South Plainfield, NJ, USA).

2022-10-26 | E-MTAB-10854 | biostudies-arrayexpress

scRNAseq of four syngeneic human melanoma cell lines (two replicate per cell line) to study mechanisms of resistance to the BRAF inhibitor vemurafenib

Project description:Three cell lines were derived from the A375 human melanoma (harbouring the BRAF v600e mutation; ATCC) after treatment with vemurafenib during a period of 4-5 weeks in the absence (MAPKi-resist Rep1/Rep2) or presence of the fatty acid oxidation inhibitors etomoxir (Etomoxir Rep1/Rep2) or ranolazine (Ranolazine Rep1/Rep2).

2023-06-20 | E-MTAB-12412 | biostudies-arrayexpress

MPS vaccination alters long-term gene expression of antigen-presenting cells in lymph nodes

Project description:Given the importance of sustained antigen presentation in maintenance of lymph node (LN) immune responses, we hypothesized that vaccine antigen availability and antigen-presenting cell (APC) populations may affect LN expansion. Compared to LNs of mice given the full MPS vaccine, LNs of mice given an MPS vaccine without antigen became prominently less enlarged and contracted sooner.To identify potential mediators of this differential, antigen-dependent response, we next focused the analysis of our scRNA-seq dataset on LN APC populations.

2024-04-05 | E-MTAB-13698 | biostudies-arrayexpress

scRNA-seq of CD45+ cells taken from the ear epidermis from K14E7 transgenic and wildtype C57/BL6 mice

Project description:Langerhans cells (LC) in skin help initiate the immune response to locally presented antigens. We performed high-resolution single-cell RNA-sequencing (scRNAseq) analysis for antigen presenting cells including LC in normal mouse skin, and in mouse skin expressing the human papillomavirus (HPV) 16 E7 oncogene. Ear skin was collected from normal and trangenic mice. Dissociated CD45+ cells were processed for scRNA-seq using the 10X Genomics Chromium 3' gene expression kit (v2).

2021-10-15 | E-MTAB-8199 | biostudies-arrayexpress

Single-cell RNA sequencing of human liver cells

Project description:To examine the heterogeneity and dynamic crosstalk of human liver cells, ~18,000 freshly isolated human liver cells from 6 donors were profiled using the 10x Genomics Chromium platform.

2021-09-29 | E-MTAB-10553 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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