Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

150 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of coding RNA from samples of 20 human individuals representing four cancers: glioma, colon cancer, liver cancer and testicular cancer, as well as three cell lines.

ABSTRACT: RNA-seq was performed of cancer samples from 20 human individuals representing four cancers: glioma, colon cancer, liver cancer and testicular cancer, as well as six samples from the three cell lines NTERA-2, U-87 MG och U-138 MG in order to study the human tissue transcriptome.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Linn Fagerberg

PROVIDER: E-MTAB-4681 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of coding RNA from tissue samples of 122 human individuals representing 32 different tissues

Project description:RNA-seq was performed of tissue samples from 122 human individuals representing 32 different tissues in order to study the human tissue transcriptome. This submission contains 27 new samples and the data from E-MTAB-1733. This dataset is part of the TransQST collection.

2015-01-14 | E-MTAB-2836 | biostudies-arrayexpress

HPA RNA-seq normal tissues

Project description:RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes. This dataset is part of the TransQST collection.

2013-12-06 | E-MTAB-1733 | biostudies-arrayexpress

RNA-Seq of frozen human brain tissue

Project description:These are three technical replicates RNA-Seq for frozen human brain tissue. They are generated for comparison with single cell RNA sequencing data that generated by the same sample and provided elsewhere.

2019-03-15 | E-MTAB-7738 | biostudies-arrayexpress

RNA-Seq of human pancreas tissue

Project description:These are three technical replicates RNA-Seq for frozen human pancreas tissue. They are generated for comparison with single cell RNA sequencing data that generated by the same sample and provided elsewhere.

2019-03-15 | E-MTAB-7740 | biostudies-arrayexpress

Identification of potential biomarkers in testicular cancer by SILAC and mass spectrometry

Project description:This study represents a proteomic resource for testis cancer with quantitative protein expression data for 5236 proteins. By quantitative mass-spectrometry-based proteomics, we compared the two Malignant germ cell tumour cell lines, TCam-2 with seminoma-like characteristics, and NTERA-2, an embryonal carcinoma-like cell line.

2019-11-12 | PXD010275 | Pride

Gene expression data for two xenograft models representing luminal-like and basal-like breast cancer

Project description:Choline (reference 1) and glucose (reference 2) was studied using HR MAS MR spectroscopy data and 105 and 38 gene transcripts were selected respectively from the microarray data to study differences between two xenograft models. Reference 1: Moestue SA et al, Distinct choline metabolic profiles are associated with differences in gene expression for basal-like and luminal-like breast cancer xenograft models, BMC Cancer 2010 Aug 17;10:433 (PMID: 20716336). Reference 2: Grinde et al., submitted The microarray data from the luminal-like and basal-like xenograft models were compared for selected genes, using Limma Bioconducotr package

2010-12-08 | E-GEOD-25915 | biostudies-arrayexpress

Cell state-dependent chromatin targeting in NUT carcinoma

Project description:ChIP-seq profiles of BRD4-NUT in HUES64 & HUES64 derived mesoderm (dME). ChIP-seq profiles of BRD4-NUT in Ntera-2 (NT2) cells & Ntera-2 (NT2) differentiated cells after 4 hr and 16 hr retinoic acid treatment..

2023-04-14 | GSE229558 | GEO

RNA-Seq characterization of select lincRNA knockout mouse models

Project description:It has become clear that long intergenic noncoding RNAs (lincRNAs) are an important layer of genome regulation. Thousands have been identified in mammals, yet only a few have been tested through genetic ablation in animal models. Of the few that have, many yields weak to unobservable phenotypes, raising the question of their in vivo relevance. To more broadly investigate the functional relevance of lincRNAs in physiological conditions, we developed a collection of 18 lincRNA knockout strains. We found that two knockout strains, linc-Sox2 and linc-Foxf1a (Fendrr), exhibit perinatal lethal phenotypes in addition to multiple developmental abnormalities. Notably, in depth analysis of a third mutant strain, linc-Brn1b-/-, revealed defects in brain development, with distinct abnormalities in class-specific generation of upper layer II/III-IV neurons in the neocortex. Thus far, we found at least 6 of 18 mutant strains exhibit distinct developmental or lethality phenotypes. Therefore, this study demonstrates that lincRNAs are required for life and play critical roles during mammalian development, highlighting the importance of studying them further to better understand the molecular mechanisms leading to disease. Minimum 2 replicates each of select wild type and lincRNA knockout embryonic and postnatal tissues for three distinct lincRNA knockout mouse strains.

2013-11-30 | E-GEOD-49581 | biostudies-arrayexpress

DNA Methylation assessment of GLO1-depleted MDA-MB-231 breast cancer cells and mouse xenografts

Project description:Oncometabolites are of the utmost importance to our understanding of tumor initiation, progression and resistance to therapy. We previously demonstrated that methylglyoxal (MG), a reactive dicarbonyl spontaneously formed in glycolytic cancer cells, unexpectedly enhanced their metastatic potential. Here, using genome-wide DNA methylation analysis, we report that MG stress induced DNA methyltransferases (DNMTs) expression resulting in DNA hypermethylation in triple negative breast cancer cells. Interestingly, we observed that DNMT3B protein was stabilized upon MG stress. Consistently, MG stressed cells demonstrated a significant loss of tumor suppressor genes as assessed using integrated analysis of methylome and RNASeq data. Both 5-AZA demethylating agent and MG scavengers triggered the re-expression of representative silenced genes. We have delineated an epigenomic signature of MG stress that effectively provided survival stratification in breast cancer patients. This study emphasizes the importance of MG stress, occurring downstream of the Warburg effect, as a major epigenetic regulator and proposes MG scavengers to reverse altered patterns of gene expression associated with MG stress pro-cancer effects.

2022-10-01 | GSE185237 | GEO

Luciferase Expressing Preclinical Model Systems Representing the Different Molecular Subtypes of Colorectal Cancer

Project description:We established combined 2D/3D, in vitro/in vivo model systems representing the heterogeneity of colorectal cancer (CRC) with regards to different molecular subtypes. Comparative characterization of stable luciferase expressing derivatives of well-established CRC cell lines, derived spheroids and subcutaneous xenograft tumors showed that the 3D-spheroid cultures resembled xenografts more closely than 2D-cultured cells do. The model systems can be used in preclinical research applications to study new therapy approaches and represents the biological heterogeneity of CRC.

2023-10-10 | GSE241569 | 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