Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell transcriptomics of precursor lung adenocarcinoma reveals intratumoral heterogeneity and shifting immune network

ABSTRACT: Single-cell transcriptomics of precursor lung adenocarcinoma reveals intratumoral heterogeneity and shifting immune network

PROVIDER: PRJNA691960 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13433500_1.fastq.gz	Fastqsanger.gz
	SRR13433500_2.fastq.gz	Fastqsanger.gz
	SRR13433600_1.fastq.gz	Fastqsanger.gz
	SRR13433600_2.fastq.gz	Fastqsanger.gz
	SRR13433700_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 670

Similar Datasets

Single-cell transcriptomics of precursor lung adenocarcinoma reveals intratumoral heterogeneity and shifting immune network

Project description:We conducted a multi-omics analysis including single-cell RNA transcriptome, single-cell T cell receptor (scTCR), whole exome sequencing and multiplex immunohistochemistry (mIHC) to decipher single cell atlas of precursor lung adenocarcinoma and mechanisms of diverse immune cells during precursor lesions development in hopes of digging out potential therapeutic targets.

2024-01-13 | GSE164789 | GEO

Intratumoral heterogeneity in cholangiocarcinoma

Project description:Intratumoral heterogeneity in cholangiocarcinoma

| PRJEB63091 | ENA

Intratumoral heterogeneity of prostate cancers

Project description:Copy number analyses of regionally separated intratumoral biopsies of prostate cancers. Intratumoral heterogeneity (ITH) leads to regional biases of the mutational landscape in a single tumor and may influence the single biopsy-based clinical diagnosis and treatment decision. To evaluate the extent of ITH in unifocal prostate cancers (PCAs) that had not been sought, we analyzed multiple regional biopsies from three PCAs using DNA copy number analyses. DNA copy number showed ITH including regional biases in the presentation of a well-known driver of TMPRSS2-ERG fusion. Our analyses identified a substantial level of genetic ITH in unifocal PCAs at the genomic levels, which should be taken into account for the curation of biomarkers in the clinical setting. Four intratumoral biopsies were obtained per tumor for three prostate cancers. Radical prostatectomy tissue from three patients with prostate cancers were obtained. Board-certified pathologists reviewed the hematoxylin&eosin stained sections and identified tumor-rich regions (> 80% purity). We selected four different areas for biopsy that were at least 5mm apart and were comprised of the most common Gleason pattern (the most common histologic patterns with minimal histologic differences). Copy number profiling was performed using Agilent 180K platform according to the manufacturer's protocol.

2014-01-18 | E-GEOD-54185 | biostudies-arrayexpress

Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features in Breast Cancer

Project description:Ductal carcinoma in situ (DCIS) is a nonobligate precursor of invasive breast cancer. Its biological features, particularly its intratumoral heterogeneity, remain obscure. Moreover, mechanism of lymph node metastasis is unclear. To address this deficiency, we performed single-cell transcriptome profiling of DCIS, invasive ductal carcinoma (IDC) and lymph node metastasis. Single-cell transcriptome analysis revealed that breast cancer exhibits intratumoral heterogeneity at the transcriptional level, defining specific functions, and that DCIS has similar heterogeneity to IDC.

2022-08-02 | GSE195861 | GEO

Sunitinib treatment exacerbates intratumoral heterogeneity in metastatic renal cancer

Project description:The aim of this study was to investigate the effect of VEGF targeted therapy (sunitinib) on intratumoral heterogeneity (ITH) in metastatic clear cell renal cancer (mRCC). 138 samples from patients with clear cell renal cell carcinoma, including biological replicates of nephrectomy samples. RNA extracted fresh frozen tissue samples.

2015-05-25 | E-GEOD-65615 | biostudies-arrayexpress

Single-cell transcriptomic analysis uncovers intratumoral heterogeneity and drug-tolerant persister in ALK-rearranged lung adenocarcinoma

Project description:Acquired drug resistance is the major therapeutic obstacle to maintenance treatment of advanced-stage non-small cell lung cancer. Lung adenocarcinoma (ADC) harboring driver mutations also showed poor response to immune checkpoint inhibitors (ICIs). Underlying mechanisms of how drug insensitivity evolves remain unclear. Here we explored the intratumoral heterogeneity of tyrosine kinase inhibitor (TKI)-resistant anaplastic lymphoma kinase (ALK)-rearranged lung ADC organoids using single-cell RNA-sequencing (scRNA-seq) transcriptomic analysis. IL-17 signaling pathway was found highly induced in a subpopulation of pre-existing ALK-TKI-resistant cells. These drug-tolerant persister (DTP) cells, also found to have high surface intracellular adhesion molecule 1 (ICAM-1) expression level, were more resistant towards ALK-TKI and expressed a higher level of cancer-stem cell transcriptional factors. Moreover, tumor cells with high ICAM-1 expression were found spatially correlated with RORɣt+ Th17 infiltration in ALK-rearranged NSCLC resected tumor tissues. In conclusion, our data revealed marked intratumoral heterogeneity in ALK-rearranged tumor, and pre-existing DTP cells may contribute to the development of drug insensitivity in ALK-rearranged lung ADC.

2023-08-09 | GSE223779 | GEO

Intratumoral heterogeneity of prostate cancers

2014-01-18 | GSE54185 | GEO

Sunitinib treatment exacerbates intratumoral heterogeneity in metastatic renal cancer

Project description:The aim of this study was to investigate the effect of VEGF targeted therapy (sunitinib) on intratumoral heterogeneity (ITH) in metastatic clear cell renal cancer (mRCC).

2015-05-25 | GSE65615 | GEO

Single-cell transcriptomic analysis uncovers intratumoral heterogeneity and drug-tolerant persister in ALK-rearranged lung adenocarcinoma

Project description:Single-cell transcriptomic analysis uncovers intratumoral heterogeneity and drug-tolerant persister in ALK-rearranged lung adenocarcinoma

| PRJNA928366 | ENA

Intratumoral heterogeneity, cell of origin and microenvironment in retinoblastoma [scRNA-seq]

Project description:Retinoblastoma (RB) is the most common primary intraocular malignancy of childhood. The diverse malignant and immune cells in tumors determine tumor progression, but the intratumoral heterogeneity, tumor microenvironment and their impact in RB remain poorly characterized. Here, we conducted transcriptomic profiles of around 70,000 cells from tumor samples of seven RB patients with pathological and clinical measurements. Fifteen cell types were identified where the majority were cone precursor-like (CP-like) and MKI67+ cone precursor (MKI67+ CP) cells. These cells expressed markers of cone precursor, suggesting that RB originated from cone precursor cells. The conversion of CP-like to MKI67+ CP led to the loss of photoreceptor function and increased cell proliferation ability in RB. By integrative copy number variation analysis, we found that two subtypes of MKI67+ CP cells were more malignant related to cell proliferation. The tumor microenvironment in RB was composed of three cell types, of which glial cells, including tumor-associated macrophages and astrocytes-like cells, created an immunosuppressive environment and promoted tumor growth and invasion by inhibiting the GALECTIN signaling pathway. Together, our study presents the first transcriptomic map of RB at a single-cell resolution and provides novel insights into the occurrence and progression of RB which will be important to the development of the future targeted therapy and immunotherapy.

2022-05-11 | GSE168434 | GEO

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