Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SmallRNAs profile in 60 Neuroendocrine Neoplasms (NEN) and 3 sera derived from NEN patients

ABSTRACT: We investigate the miRNA expression profiles with the attempt to identify deregulated molecules useful as NEN biomarkers. SmallRNA-Seq was performed allowing the identification of miRNAs commonly expressed in all samples. Three sera from the same samples were also sequenced.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Domenico Palumbo

PROVIDER: E-MTAB-11598 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-Seq of 60 Neuroendocrine Neoplasm (NEN) samples with different grade and primary site

Project description:The RNA isolated from 60 Neuroendocrine Neoplasm (NEN) was analysed to identify differentially expressed transcripts and fusion transcripts. Library preparation was performed using two different kit: TruSeq Stranded Total RNA (Illumina) for frozen samples and extracted RNAs, and TruSeq RNA Exome (Illumina) for FFPE samples.

2022-06-30 | E-MTAB-11599 | biostudies-arrayexpress

Multigene panel test in 44 Homo sapiens patients with either digestive system neuroendocrine Neoplasm (NEN) or medullary thryoid gland carcinoma samples

Project description:The DNA isolated from 44 either frozen or FFPE Neuroendocrine Neoplasm (NEN) was analysed by NGS, to identify genes more likely to be subject to sequence variations among 523 cancer-related ones.

2022-06-30 | E-MTAB-11529 | biostudies-arrayexpress

Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA

Project description:Comparison of the genomic profiles of urinary cellular DNA and cell-free DNA (cfDNA) from the urine to matched diagnostic formalin-fixed paraffin embedded (FFPE) tumour DNAs for 23 well-characterised UBC patients.

2015-12-31 | E-MTAB-3841 | biostudies-arrayexpress

miRNA array of patients with Pulmonary Arterial Hypertension

Project description:Comparison of miRNA expression between patients with idiopathic and systemic sclerosis PAH and healthy controls and systemic sclerosis without PAH

2021-06-01 | E-MTAB-10425 | biostudies-arrayexpress

Circulating Dirofilaria immitis microRNAs in dog plasma

Project description:We report the presence of circulating miRNAs released by the filarial nematode Dirofilaria immitis into the host (Canis familiaris) bloodstream. MiRNA deep-sequencing combined with bioinformatics revealed over 200 mature miRNA sequences of potential nematode origin in Dirofilaria immitis-infected dog plasma in two independent analyses

2014-10-03 | E-GEOD-60170 | biostudies-arrayexpress

Illumina methylation EPIC arrays of human blood at baseline and after 18 months of dietary interventions

Project description:To highlight molecular mechanisms underlying the beneficial metabolic effects of a Mediterranean (MED) diet, a MED diet enriched in polyphenols and reduced in red/processed meat (greenMED), and a diet with healthy dietary guidelines (HDG), we analyzed their effects on the methylome in the 18-month DIRECT PLUS randomized controlled trial. The methylation arrays contains individuals from the three intervention arms (MED, greenMED, HDG) for baseline (T0). We will gladly provide further metadata upon request.

2023-07-26 | E-MTAB-12527 | biostudies-arrayexpress

miRNA seq of kidney tissues from amyloidosis affected and healthy Abyssinian cats

Project description:Five kidney sections of 10 μm of thickness were sliced from each FFPE block of three amyloidosis affected and three healthy cats. The total miRNAome was isolated using the miRNeasy FFPE kit by Qiagen. A total amount of 200ng of extracted miRNA/sample was sequenced using the smallRNA-seq kit by Illumina and the Illumina NextSeq500 platform. The read length obtained was 1x75bp for a total of 30 million reads. The quality control of the reads was assessed with FastQC and the adapter sequences were removed using Cutadapt.

2020-12-31 | E-MTAB-8556 | biostudies-arrayexpress

miRNA expression in human chondrocyte subtypes

Project description:Frozen blocks of human embryonic limb tissue were sectioned and laser capture microdissected to collect three human chodrocyte tissues - precursor, differentiated and hypertrophic chondrocytes.Total RNA including miRNAs was isolated and analyzed using Applied Biosystems OpenArrayM-BM-. Real-Time PCR system. RT-PCR miRNA expression profiling. miRNA expression from three chondrocyte sub types - precursor, differentiated and hypertrophic chondrocytes were analyzed using TaqManM-BM-. OpenArrayM-BM-. Human MicroRNA Panel.

2013-10-23 | E-GEOD-49152 | biostudies-arrayexpress

LIN28A modulates splicing and gene expression programs in breast cancer cells [RNA-Seq]

Project description:The goals of this study were to identify LIN28 downstream gene targets in breast cancer cells. We use a subclone of the MCF-7 breast cancer cell line, MCF-7M as our model system. Methods: mRNA profiles from MCF-7M breast cancer cells treated with siRNA against non-targeting control (NT), LIN28, hnRNP A1, LIN28 and hnRNPA1 (LIN28A1) for 72 hrs were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, we mapped over 200 million sequence reads per sample to the human genome (build h19). Each of the four groups had two biological replicates. We developed a custom method to identify alternative splicing events and identified 111 genes with significant (FDR<0.05) differential splicing for LIN28 depleted cells compared to non-targeting siRNA control, as well as 249 and 182 genes for hnRNP A1 and LIN28A1 respectively. RNA-seq data were validated with by qRT–PCR analysis of a subset of genes. Conclusions: Results reveal that LIN28 regulates alternative splicing and steady state mRNA expression of genes implicated in aspects of breast cancer biology. Notably, cells lacking LIN28 undergo significant isoform switching of the ENAH gene, resulting in a decrease in the expression of ENAH exon 11a isoform. Expression of ENAH isoform 11a has been shown to be elevated in breast cancers that express HER2. mRNA profiles of MCF-7M cells treated with siRNA for NT control, LIN28, hnRNP A1, and LIN28 plus hnRNP A1 (A1) (LIN28A1) were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000

2015-07-27 | E-GEOD-71012 | biostudies-arrayexpress

Next Generation Sequencing (NGS) comparison of two MVT1 cells subpopulations, CD24- cells and CD24+ cells

Project description:The goal of this study is to compare the transcriptome of the 2 MVT1 subpopulations in order to identify new genes and pathways that stands beyond the CD24+ aggressive phenotype mRNA profiles of CD24- and CD24+ cells were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500

2015-05-12 | E-GEOD-68746 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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