Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Somatic Mutational Landscape of Wild Populus trichocarpa tree [ncRNA-seq]

ABSTRACT: Somatic Mutational Landscape of Wild Populus trichocarpa tree [ncRNA-seq]

PROVIDER: PRJNA549498 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9321802.fastq.gz	Fastqsanger.gz
	SRR9321803.fastq.gz	Fastqsanger.gz
	SRR9321804.fastq.gz	Fastqsanger.gz
	SRR9668950.fastq.gz	Fastqsanger.gz
	SRR9668951.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 15

Similar Datasets

Somatic Mutational Landscape of Wild Populus trichocarpa tree [ncRNA-seq]

Project description:This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

2020-08-19 | GSE132938 | GEO

The somatic mutational landscape of thyroid cancer in patients with germline PTEN mutations

Project description:The somatic mutational landscape of thyroid cancer in patients with germline PTEN mutations

| PRJNA1112909 | ENA

The somatic mutational landscape of thyroid cancer in patients with germline PTEN mutations

Project description:The somatic mutational landscape of thyroid cancer in patients with germline PTEN mutations

| PRJNA1112910 | ENA

Somatic Mutational Analysis by Exome Sequencing Endometrial Carcinosarcomas

Project description:Somatic Mutational Analysis by Exome Sequencing Endometrial Carcinosarcomas

| PRJNA326037 | ENA

Relapsed Acute Lymphoblastic Leukemia (ALL): Mutational Landscape

Project description:Relapsed Acute Lymphoblastic Leukemia (ALL): Mutational Landscape

| PRJNA597498 | ENA

Relapsed Acute Lymphoblastic Leukemia (ALL): Mutational Landscape

Project description:Relapsed Acute Lymphoblastic Leukemia (ALL): Mutational Landscape

| PRJNA597499 | ENA

Individualized proteogenomics reveals mutational landscape of melanoma patients in response to immunotherapy

Project description:Immune checkpoint inhibitors are used to restore or augment antitumor immune response and show great promise in treatment of melanoma and other types of cancers. However, only a relatively small percentage of patients are fully responsive to immune checkpoint inhibition, mostly due to tumor heterogeneity and primary resistance to therapy. Both of these features are largely driven by accumulation of patient-specific mutations, pointing to the need for personalized approaches in diagnostics and immunotherapy. Proteogenomics integrates patient-specific genomic and proteomic data to study cancer development and resistance mechanisms, as well as tumor heterogeneity in individual patients. Here, we use a proteogenomic approach to characterize the mutational landscape of samples derived from four clinical melanoma patients at the genomic, proteomic and phosphoproteomic level. Integration of datasets enabled identification and quantification of an extensive number of sample-specific amino acid variants, among them many were not previously reported in melanoma. We detected a disproportional number of alternate peptides between treated and untreated (naïve) samples with a high potential to influence signal transduction. This is one of the first proteogenomic study designed to study the mutational landscape of patient-derived melanoma tissue samples in response to immunotherapy.

2022-02-16 | PXD028700 | Pride

The mutational landscape of a Prion-like domain

Project description:The mutational landscape of a Prion-like domain

| PRJNA526635 | ENA

Mutational Landscape of Lethal Castrate Resistant Prostate Cancer

Project description:Mutational Landscape of Lethal Castrate Resistant Prostate Cancer

| PRJNA177193 | ENA

Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia

Project description:Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by differentiation block at the promyelocyte stage. Besides the presence of chromosomal rearrangement t(15;17) leading to formation of PML-RARA fusion, other genetic alterations have also been implicated in APL. Here, we performed comprehensive mutational analysis of primary and relapse APL to identify somatic alterations which cooperate with PML-RARA in the pathogenesis of APL. We explored the mutational landscape using whole-exome (n=12) and subsequent targeted sequencing of 398 genes in 153 primary and 69 relapse APL. Both primary and relapse APL harbored an average of eight non-silent somatic mutations per exome. We observed recurrent alterations of FLT3, WT1, NRAS and KRAS in the newly diagnosed APL, while mutations in other genes commonly mutated in myeloid leukemia were rarely detected. The molecular signature of APL relapse was characterized by emergence of frequent mutations in PML and RARA genes. Our sequencing data also demonstrates incidence of loss-of-function mutations in previously unidentified genes, ARID1B and ARID1A, both of which encode for key components of the SWI/SNF complex. We show that knockdown of ARID1B in APL cell line, NB4, results in large scale activation of gene expression and reduced in vitro differentiation potential. Studying the effects of silensing ARID1B gene in NB4 cell lines

2016-02-17 | E-GEOD-77946 | 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