Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comprehensive RNA-Seq Dataset for Pan-Cancer Tumor Classification

ABSTRACT: The following consists of an RNA-Seq cohort comprised of samples from patients diagnosed with various tumor types across the pan-cancer spectrum. Collected at diagnosis, these samples serve as a resource for tumor classification using machine learning classifiers. Process count tables are provided. This cohort can assist researchers in exploring molecular signatures and facilitate accurate classification across diverse malignancies.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: John Baker-Hernandez

PROVIDER: E-MTAB-14038 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Analysis of cardiac miRNA expression in the early neonatal period

Project description:The regenerative capacity of the mammalian heart is lost quickly after birth when cardiomyocytes stop dividing and undergo cell cycle arrest. Thus, the adult mammalian heart lacks the ability to heal itself to any appreciable amount after ischemic injury such as myocardial infarction. Heart growth begins during fetal life with the first phase of DNA synthesis that is exclusively associated with cardiomyocyte proliferation. This process proceeds until 12 hours after birth and is defined as 0 days in our submitted samples. Cardiomyocytes division is undetectable at neonatal day 1. To analyze the molecular mechanisms responsible for cessation of cardiomyocyte proliferation, we performed genome-wide miRNA microarray profiling by comparing postnatal days 0 vs 1d.This revealed a profile of 8 significantly downregulated miRNAs in the proliferative DKO hearts (versus vehicle-injected control), that were enriched for mRNA targets involved in cell cycle regulation. In vitro studies have demonstrated that knockdown of these 8 miRNAs in neonatal rat cardiomyocytes can increase the occurrence of cytokinetic events. Ultimately, we aim to inject antagomirs targeting these miRNAs into mice post-myocardial infarction to determine the effect of these miRNAs on heart function and cardiomyocyte proliferation in vivo.

2022-01-30 | E-MTAB-9256 | biostudies-arrayexpress

ChIP seq of H3K4me3 and pan-H3 in WT and jhd2Î? Saccharomyces cerevisiae cells

Project description:We describe the landscape of H3K4me3 in WT and jhd2Î? cells in YAR media by ChIP seq To determine the contribution of Jhd2 to the H3K4me3 landscape in respiring yeast cells, we performed H3K4me3 ChIP and normalized to pan-H3 ChIP signal.

2016-08-09 | E-GEOD-85320 | biostudies-arrayexpress

Efficacy of trametinib and dabrafenib associated with radioactive iodine for the treatment of refractory metastatic differentiated thyroid cancer (KRAS cohort)

Project description:Efficacy of a selective MEK (trametinib) and BRAFV600E (dabrafenib) inhibitors associated with radioactive iodine (RAI) for the treatment of refractory metastatic differentiated thyroid cancer with RAS (current cohort) or BRAFV600E mutation. To evaluate the objective response rate according to RECIST criteria in thyroid cancer patients with metastatic radioactive iodine (RAI) refractory disease, 6 months after a treatment combining in each arm of the phase II trial (patients with RAS mutation or patients with BRAFV600E mutation): - Arm A: 6 weeks of trametinib followed by RAI treatment (5.5 GBq following rhTSH) in patients with RAS mutation - Arm B: 6 weeks of trametinib plus dabrafenib followed by RAI treatment (5.5 GBq following rhTSH) in patients with BRAFV600E mutation

2023-09-01 | E-MTAB-12900 | biostudies-arrayexpress

IGR_U985_CLL_Exome

Project description:Chronic lymphocytic leukemia (CLL), the most frequent adult leukemia in western countries, is a clonal accumulation of mature B-lymphocytes and its natural history is yet unclear. By using sequencing and cellular biology approaches on a cohort of CLL patient samples, we show here that acquired CLL mutations are observed in hematopoietic multipotent progenitor fractions in the majority of patients. These early CLL mutations include recurrent inactivating mutations in NFKBIE (10.7%) and missense mutations in BRAF (3.6%) and EGR2 (8.3%). Functional analyses demonstrated that BRAF-G469R affects lymphoid differentiation and transforms the T-cell lineage in vivo. In addition, the EGR2 recurrent mutations were associated with transcriptional activation of EGR2 target genes in patients and cell cycle abnormality in cellular model. Our findings indicate that CLL may develop from an initial infra-clinic, pre-leukemic phase affecting immature hematopoietic cells. The aim of this study is to compare exome sequences from tumor cells and T-lymphocytes in order to predict somatic mutations in 24 CLL patients (17 IGHV-unmutated and 7 IGHV-mutated). Enriched exome fragments were subjected to massively parallel sequencing using HiSeq 2000 (Illumina).

2015-01-12 | E-MTAB-1775 | biostudies-arrayexpress

Epigenetic activation of a subset of mRNAs identified using polyribosome microarray analysis

Project description:Background: Translation deregulation is an important mechanism that causes aberrant cell growth, proliferation and survival. eIF4E, the mRNA 5 prime capâ??binding protein, plays a major role in translational control. To understand how eIF4E affects cellular proliferation and cell survival, we identified mRNA targets that are translationally responsive to eIF4E. Methodology/ principal findings: Microarray analysis of polysomal mRNA from an eIF4E-inducible NIH 3T3 cell line was performed. Induction of eIF4E expression resulted in increased translation of a defined set of mRNAs; many of the mRNAs are novel targets, including those that encode large- and small-subunit ribosomal proteins and cell growthâ??related factors. eIF4E overexpression also led to augmented translation of mRNAs encoding anti-apoptotic proteins, which conferred resistance to endoplasmic reticulumâ??mediated apoptosis. Conclusions/ significance: Our results shed new light on the mechanisms by which eIF4E prevents apoptosis and transforms cells. Downregulation of eIF4E and its downstream targets is a therapeutic option for the development of novel anti-cancer drugs. Keywords: time course Comparison of total and polysomal RNA upon eIF4E iinduction in NIH3T3/parental and NIH3T3/eIF4E cells Each of the following pairs were generated from one hybridization: GSM153931 GSM153932 GSM153933 GSM153934 GSM153935 GSM153936 GSM153937 GSM153938 GSM153939 GSM153940 GSM153941 GSM153942 GSM153943 GSM153944 GSM153945 GSM153946 GSM153947 GSM153948 GSM153949 GSM153950 GSM153951 GSM153952 GSM153953 GSM153954 GSM153955 GSM153956 GSM153957 GSM153958 GSM153959 GSM153960 GSM153961 GSM153962

2010-06-11 | E-GEOD-6639 | biostudies-arrayexpress

Expression data from hyperplastic polyps and normal colonic mucosa from patients with familial and sporadic HPPS

Project description:Expression data from hyperplastic polyps and normal colonic mucosa from patients with familial and sporadic hyperplastic polyposis syndrome (HPPS). We aim to characterize at a molecular level a cohort of hyperplastic lesions from HPPS patients with and without family history. RNA from hyperplastic polyps and normal colonic mucosa (proximal and distal) from patients with familial and sporadic HPPS were included in this study. Total RNA was isolated from each tissue sample, quantified and its quality evaluated. cRNA preparation, hybridization and analysis of results was performed according to Affymetrix recommendations. cRNA was hybridised in the GeneChip array (Human Genome U133 Plus 2.0, Affymetrix), and the intensity was measured.

2010-12-01 | E-GEOD-19963 | biostudies-arrayexpress

Expression data for Vanderbilt triple-negative breast cancer subtype classification

Project description:This study developed a triple-negative breast cancer (TNBC) surrogate subtype classification that represents TNBC subtypes based on the Vanderbilt subtype classification The web-based subtyping tool TNBCtype was used to classify the TNBC cohort into Vanderbilt subtypes

2023-03-04 | GSE226289 | GEO

Expression array for Multi-omics molecular profiling of primary prostate adenocarcinoma

Project description:Multi-omics molecular profiling was performed on post-radical prostatectomy material from a cohort of 132 patients with localized prostate adenocarcinoma. Unsupervised classification techniques were used to build a comprehensive classification of prostate tumours based on three molecular levels: DNA copy number, DNA methylation, and mRNA expression.

2018-06-24 | E-MTAB-6128 | biostudies-arrayexpress

Exploring the spectrum of somatically acquired genomic lesions in HCLc by WGS

Project description:Whole genome sequencing of 10 HCLc tumor and matched-germline T cells. Genomic DNA from highly purified HCLc tumor and T cell populations were utilized for library preparation using NEBNext Ultra DNA library prep kit. Sequencing was performed as 150 bp paired end sequencing using four lanes of an Illumina HiSeq4000 to an average depth of 12X. Reads from each library were aligned to the human reference genome GRCh37 using BWA-MEM (v0.7.12). The analysis of somatic genetic alterations in WGS data from tumor-germline pair HCLc samples was divided based on the nature of the mutation, as follow: single-nucleotide variants (SNVs), indels, CNAs and SVs. Moreover, COSMIC mutational signatures and subclonal architecture was inferred for each tumor.

2023-01-01 | E-MTAB-12046 | biostudies-arrayexpress

SNP array Multi-omics molecular profiling of primary prostate adenocarcinoma

2018-07-09 | E-MTAB-6127 | biostudies-arrayexpress