Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Multiple lymph nodes sequencing in advanced primary lung cancer

PROVIDER: PRJNA316182 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3310050_1.fastq.gz	Fastqsanger.gz
	SRR3310050_2.fastq.gz	Fastqsanger.gz
	SRR3310060_1.fastq.gz	Fastqsanger.gz
	SRR3310060_2.fastq.gz	Fastqsanger.gz
	SRR3310070_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 110

Similar Datasets

Single cell RNA sequencing of lung adenocarcinoma

Project description:We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas of lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

2020-03-27 | GSE131907 | GEO

CIT - Homo sapiens - APUP - Genomic aberrations in Lung Adenocarcinoma in Never Smokers

Project description:41 lung adenocarcinoma from never-smokers hybridized on Illumina SNP arrays on 13 HumanCNV370-Quadv3 chips. High-resolution array comparative genomic hybridization analysis of lung adenocarcinoma in 41 never smokers for identification of new minimal common regions (MCR) of gain or loss. The SNP array analysis validated copy-number aberrations and revealed that RB1 and WRN were altered by recurrent copy-neutral loss of heterozygosity.The present study has uncovered new aberrations containing cancer genes. The oncogene FUS is a candidate gene in the 16p region that is frequently gained in never smokers. Multiple genetic pathways defined by gains of MYC, deletions of RB1 and WRN or gains on 7p and 7q are involved in lung adenocarcinoma in never smokers. A 'Cartes d'Identite des Tumeurs' (CIT) project from the French National League Against Cancer (http://cit.ligue-cancer.net) 41 samples hybridized on Illumina SNP arrays. Submitter : Fabien PETEL petelf@ligue-cancer.net . Project leader : Pr Pierre FOURET pierre.fouret@psl.aphp.fr

2011-07-28 | E-TABM-1169 | biostudies-arrayexpress

Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V

Project description:Lung cancer is the leading cause of cancer death both in men and women. Tumor heterogeneity is an impediment to targeted treatment of all cancers, including lung cancer. Here, we sought to characterize changes in tumor proteome and phosphoproteome by longitudinal, prospective collection of tumor tissue of an exceptional responder lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for more than seven years with HER2-directed therapy in combination with chemotherapy. We employed “Super-SILAC” and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and ten different metastatic progressive lymph nodes collected across a span of seven years, including five lymph nodes procured at autopsy. We identified specific signaling networks enriched in lung compared to the lymph node metastatic sites. We correlated the changes in protein abundance with changes in copy number alteration (CNA) and transcript expression. To further interrogate the mass spectrometry data, patient-specific database was built incorporating all the somatic variants identified by whole genome sequencing (WGS) of genomic DNA from the lung, one lymph node metastatic site and blood. An extensive validation pipeline was built for confirmation of variant peptides. We validated 360 spectra corresponding to 55 germline and 6 somatic variant peptides. Targeted MRM assays demonstrated expression of two novel variant somatic peptides, CDK12 G879V and FASN-R1439Q, with expression in lung and lymph node metastatic sites, respectively. CDK12 G879V mutation likely results in a nonfunctional kinase and knockdown of CDK12 in lung adenocarcinoma cells increased chemotherapy sensitivity, explaining the complete resolution of the lung metastatic sites in this patient.

2019-01-07 | PXD010779 | Pride

single-cell RNA sequencing reveals the mechanism of human breast cancer metastasis

Project description:To obtain more information about the lymph node metastasis of breast cancer cells, we selected the matched primary breast cancer (PC), positive lymph nodes (PL), and negative lymph nodes (NL) of the same patient to perform integrated analysis. The PC, PL, NL samples were analysed with single-cell RNA sequencing.

2021-08-08 | GSE158399 | GEO

Homo sapiens

Project description:Transcription Profiles of Regulatory T Cells in Follicular Lymphoma Lymph Nodes, Normal Lymph Nodes and Reactive Lymph Nodes

| PRJNA299009 | ENA

Homo sapiens

Project description:16s rRNA sequencing of lymph nodes of head and neck cancer

| PRJNA663453 | ENA

Multi-omic (microbiome, metabolome, and immunome) study of peritumoral lymph nodes in gastric and colorectal cancer.

Project description:Interventions: Positive lymph nodes around gastric cancer:None;Negative lymph nodes around gastric cancer:None;Positive lymph nodes around colorectal cancer:None;Negative lymph nodes around colorectal cancer:None Primary outcome(s): Lymph nodes pathology diagnosis;Lymph nodes high-throughput sequencing;Metabonomics of lymph nodes;Immunomics of lymph nodes Study Design: Sequential

| 89365 | ecrin-mdr-crc

Homo sapiens

Project description:Gene expression profile of purified tumor cells from primary breast cancer tumor tissues and metastatic lymph nodes

| PRJNA143467 | ENA

Single-cell RNA sequencing reveals the mechanism of human breast cancer metastasis

Project description:To obtain more information about the lymph node metastasis of breast cancer cells, we selected the matched primary breast cancer (PC) and 2 lymph nodes (LN) of 5 patients to perform integrated analysis. The PC, LN samples were analysed with single-cell RNA sequencing.

2021-10-13 | GSE180286 | GEO

Genetic Analysis to Interrogate Tumor Heterogeneity in Lung Adenocarcinoma

Project description:<p>We employed next-generation sequencing to identify somatic alterations in multiple metastatic sites from an "exceptional responder" lung adenocarcinoma patient during his seven year course of ERBB2-directed therapies. The degree of heterogeneity was unprecedented, with ~1% similarity between somatic alterations of the lung and lymph nodes. One novel translocation, PLAG1-ACTA2, present in both sites, up-regulated ACTA2 expression. ERBB2, the predominant driver oncogene, was amplified in both sites, more pronounced in the lung, and harbored an L869R mutation in the lymph node. Functional studies demonstrated increased proliferation, migration, metastasis, and resistance to ERBB2-directed therapy due to L869R mutation and increased migration due to ACTA2 overexpression. Within the lung, a nonfunctional CDK12, due to a novel G879V mutation, correlated with down-regulation of DNA damage response genes, causing genomic instability, and sensitivity to chemotherapy. We propose a model whereby a sub-clone metastasized early from the primary site and evolved independently in lymph nodes.</p>

| phs001159 | dbGaP

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