Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

7f1ec647-2c6a-45c9-9b5f-c4f095f6c99b - samples

ABSTRACT: Chromium 10x scRNA of 6 metastatic colorectal cancer organoids

PROVIDER: EGAD00001008734 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Clonally expanded EOMES+ Tr1-like cells in primary and metastatic tumors associate with disease progression

Project description:We performed single-cell transcriptome analysis with the 10X Genomic Chromium platform of CD4+ T cells infiltrating human primary and metastatic colorectal cancer (CRC) and non-small-cell lung cancer (NSCLC). Datasets derive from fresh samples collected and immediately processed by cell sorting and single-cell isolation 10X protocol. A total number of 10000 cells per sample was analyzed by scRNA-seq.

2021-04-28 | E-MTAB-7006 | biostudies-arrayexpress

Spatial transcriptomics of human colorectal cancer liver metastatic samples

Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Spatial transcriptomics was performed using 10x Genomics Visium on colorectal cancer liver metastatic patient samples.

2025-04-22 | E-MTAB-13655 | biostudies-arrayexpress

Single cell RNA-seq of hiPSC-derived kidney organoids differentiated within self-assembling peptide hydrogels and the animal-derived matrix Matrigel

Project description:scRNA-seq was used to characterise hiPSC-derived kidney organoids differentiated within fully synthetic self-assembling peptide hydrogels of variable mechanical strengths and compare these to organoids differentiated within the animal-derived matrix, Matrigel. Organoids were matured in the respective matrices until day 24 of differentiation and 6 organoids per support matrix were then pooled and dissociated using the cold-active protease from Bacillus licheniformis. Cells were processed on the 10x Genomics Chromium platform using the Single-Cell 3’ v3.1 protocol. The NextSeq500 (Illumina) was used to sequence the libraries generated and initial processing of the data was carried out using the 10X Genomic Cell Ranger v3.1.0 pipeline.

2022-10-31 | E-MTAB-11149 | biostudies-arrayexpress

Single-cell RNA-seq of PBMCs from HCC patients pre- and post-curative therapy

Project description:This dataset contains processed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) collected from six hepatocellular carcinoma (HCC) patients, before and after curative therapy. Samples were profiled using the 10x Genomics Chromium platform. The dataset includes gene expression matrices and associated metadata for 12 samples (6 pre-therapy, 6 post-therapy). These data support the analysis of peripheral immune cell dynamics in response to tumor removal

2026-01-13 | E-MTAB-16408 | biostudies-arrayexpress

Single-cell RNA sequencing of human salivary glands and organoids

Project description:We performed single-cell RNA sequencing (scRNA-seq) on human salivary gland tissues and derived organoids to investigate their cellular composition, differentiation states, and regenerative potential. Four samples were dissociated into single-cell suspensions and processed using the 10X Genomics Chromium platform.

2025-12-19 | GSE303450 | GEO

Longitudinal Single-Cell Transcriptomic Profiling of the Peripheral Immune Response in Ischaemic Stroke

Project description:This dataset consists of single-cell RNA sequencing (scRNA-seq) data derived from Peripheral Blood Mononuclear Cells (PBMCs) of two ischaemic stroke patients (P66 and P79). The study follows a longitudinal design to identify temporal changes in the systemic immune response, with samples collected at two timepoints: the acute in-patient stage (V1) and at 6-9 months follow-up (V3). Here, four samples (P66_V1, P66_V3, P79_V1, P79_V3) were multiplexed using the 10x Genomics CellPlex protocol and processed as a single pool. Approximately 33,000 cells were loaded onto a 10x Chromium Controller using the Chromium Next GEM Single Cell 5' Reagent Kit. This specific library represents the Gene Expression (GEX) portion of a multi-modal immune profiling experiment. The primary objective of this study was to assess the dynamics of the circulating immune compartment following ischaemic stroke.

2026-03-05 | E-MTAB-16654 | biostudies-arrayexpress

Single-cell RNA sequencing of Lung Squamous Cell Carcinoma Assosciated with Idiopathic Pulmonary Fibrosis

Project description:This dataset contains single-cell RNA sequencing (scRNA-seq) data from two patients with lung squamous cell carcinoma (LUSC) associated with idiopathic pulmonary fibrosis (IPF). Tumor and adjacent lung tissues (within and outside UIP lesions) from two patients were snap-frozen, fixed, and processed using the 10x Genomics Chromium Fixed RNA Profiling workflow. Libraries were sequenced on an Illumina NovaSeq 6000 platform and processed using Cell Ranger (10x Genomics).

2026-03-02 | GSE305872 | GEO

Transcriptomic profiling of genetically engineered mouse tumors using SOCRATES

Project description:This dataset contains single-cell RNA sequencing data from murine colorectal tumors engineered using the SOCRATES platform, a CRISPR-based multiplex genome engineering system. Tumors were initiated in genetically engineered mouse models via lentiviral delivery of pooled sgRNAs targeting key driver genes in colorectal cancer, including Apc, Kras, Trp53, Smad4, and Pten. Following tumor formation, tissues were dissociated and processed using the 10x Genomics Chromium platform. Cells were multiplexed using TotalSeq-B hashing antibodies, and both gene expression and hashtag libraries were generated using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1. Sequencing was performed on a NovaSeq6000 platform. Fastq files, raw counts (gene-by-cell matrix), and associated cell metadata (including sample identifiers, genotypes, classification categories, and run information) are provided. The individual reads of the respective tumours need to be demultiplexed and assigned to the individual samples. In the raw counts file and the cell metadata file, the individual samples are already demultiplexed and the cells can be assigned with the metadata file. This dataset enables the exploration of genotype-dependent transcriptional states, and microenvironmental composition at single-cell resolution.

2026-05-01 | E-MTAB-15044 | biostudies-arrayexpress

Single-cell RNA-sequencing analysis for the molecular taxonomy of primate hippocampus after sevoflurane exposure

Project description:We thus isolated hippocampus from rhesus macaques and performed single-cell RNA-sequencing analysis. The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA).

2023-06-12 | GSE153598 | GEO

Single-cell RNA-seq analysis of patient derived organoids from colorectal cancers

Project description:Organoids were collected and signle cells were prepared in TrypLE. 10x Genomics Chromium was used for single cell capture and cDNA preparations according to the Single Cell 3' v3 Protocol recommended by the manufacturer.

2025-11-20 | E-MTAB-16177 | 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