Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNA-Seq of tumour using different dissocation condition

ABSTRACT: scRNA-Seq of tumour using different dissocation condition

PROVIDER: PRJNA586874 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10380525.fastq.gz	Fastqsanger.gz
	SRR10380526.fastq.gz	Fastqsanger.gz
	SRR10380527.fastq.gz	Fastqsanger.gz
	SRR10380528.fastq.gz	Fastqsanger.gz
	SRR10380529.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

scRNA-Seq of tumour using different dissocation condition

Project description:We performed single-cell RNA-Seq to study the effect of temperature and the transcriptional inhibitor ActD, on the representation of individual cellular populations within the tumour sample. We collected tumour tissue after 10 days of the growth, dissociated it and analysed it using scRNA-Seq. The ScRNA-Seq analysis contained 654 cells, which were divided into four main cellular types: Tumour cells, Macrophages, T cells and Natural killer (NK) cells.

2024-10-31 | GSE139681 | GEO

Detecting circulating tumour DNA from gestational trophoblastic tumour using common SNPs

Project description:Gestational tumour diagnosis using circulating tumour DNA

| PRJEB49976 | ENA

Investigation of different gene expression of putative tt mutants under AIC condition using RNA-seq

Project description:Investigation of different gene expression of putative tt mutants under AIC condition using RNA-seq

| PRJNA531896 | ENA

scRNA-seq of mESC and mouse CD4+ cells using different buffers and enzymes

Project description:scRNA-seq of mESC and mouse CD4+ cells using different buffers and enzymes

| PRJEB39616 | ENA

scRNA-seq and differential expression analyses of metastatic melanoma cells before, during and after tumour escape

Project description:Highly invasive integrin and protease-independent amoeboid migration is often employed by cancer cells at the invasive front, though little is known about the transcriptomic changes underlying the switch to an amoeboid migratory mode. Using a metastatic melanoma cell line expressing photoconvertible Dendra2 protein (WM983c-D2), tumour spheroids were cultured in 3D collagen matrices and imaged over time. Spheroids grown from WM983c-D2 cells generate cells of three distinct phenotypes: 1) compact, non-invading cells organised at the spheroid surface with no visual cell protrusions, hereafter termed ‘epithelial’; 2) cells still attached to the spheroid periphery that have commenced tumour escape, exhibiting cellular protrusions and an elongated phenotype, hereafter termed ‘escaping’; 3) singly migrating cells exhibiting a rounded phenotype and no lamellipodia consistent with amoeboid cell migration, hereafter termed 'amoeboid'. Individual amoeboid and escaping cells, as well as groups of epithelial cells at the spheroid edge were photoconverted and single cell sorted via FACS following enzymatic digestion of the collagen matrix. 10 Epithelial, 12 escaping and 13 amoeboid cells were subjected to scRNA-seq and differential expression analyses in order to identify changes in gene expression as melanoma cells convert from a non-invasive epithelial state to invasive amoeboid cells.

2022-05-21 | E-MTAB-11722 | biostudies-arrayexpress

Clonality analysis in breast tumour pairs using aCGH data

Project description:Clonality analysis in breast tumour pairs using aCGH data

| PRJNA429345 | ENA

Investigation on different small RNA expression of TT19 suppressors under anthocyanin induction condition (AIC) using Small RNA-seq

Project description:Investigation on different small RNA expression of TT19 suppressors under anthocyanin induction condition (AIC) using Small RNA-seq

| PRJNA564017 | ENA

Education of tumour-associated macrophages by the tumour matrisome inhibits immune surveillance

Project description:Metastatic ovarian tissues represent a complex tumour microenviroment. We analysed the tumour matrisome and immune cell environment in 39 metastatic ovarian tissues. We developed a disease score system, which positively correlated with the tumour matrisome. A distinct matrisome signature was identfied with increasing disease. Immune abundance and phenotype positively correaletd with tumour matrisome components. We developed a decellularised tissue model using metastatic ovarian omental tissues that maintained ECM protein content and architecture and cultured human blood-derived macrophages derived from four different donors. Monocytes cultured on high diseased tissues differerntiated into a distinct macrophage population, different from uninvovled (low disease) samples. Tumour ECM cultured macrophages had pro-tumorgenic phenotype and function.

2023-03-24 | GSE186145 | GEO

Using a xenograft model and RNA-seq to differentiate between the tumour and tumour microenvironment transcriptome

Project description:In addition to the tumour cells, breast tumours contain other cell types such as fibroblasts, adipocytes, inflammatory and immune cells. Together with the extracellular matrix, these non-tumour cells compose the tumour microenvironment (TME). Complex interactions occur between tumour cells and the TME that can inhibit or stimulate tumour cell growth, metastasis and/or chemoresistance. While treatment of tumours with chemotherapeutic agents such as Abraxane, leads to apoptosis of tumour cells, it can also have consequences for the cellular makeup and transcriptional profile of the TME and these, like the increased infiltration of macrophages, may have detrimental effects. Transcriptome profiling of whole tumours from mice injected with tumour cell lines and treated with combinations of chemotherapeutic drugs has provided novel insights into pathways affected by different agents and diagnostic signatures. However, differences in the cellular composition of tumours from treated mice can have confounding effects and increase variation in whole tumour transcriptomes. To be able to examine the effects of co-treatment of Abraxane with another drug, we performed RNA-seq on tumours from mice injected with the human breast cancer cell line MDA-MB-231. We then separated reads mapped to the human and mouse genomes in silico, creating tumour and TME transcriptomes for control, Abraxane, drug and combination treated mice. Separation of the tumour and TME profiles revealed that while in the tumour cells, co-addition of the drug potentiated Abraxane’s inhibitory effect on cell cycle genes and promotional effect on antigen presentation genes, in the TME it inhibited genes involved in the inflammation and migration responses and promoted genes involved in lipid and xenobiotic metabolism.

2020-10-01 | GSE121119 | GEO

Using a xenograft model and RNA-seq to differentiate between the tumour and tumour microenvironment transcriptome

Project description:Using a xenograft model and RNA-seq to differentiate between the tumour and tumour microenvironment transcriptome

| PRJNA495798 | ENA