GEO series

Exosomal miR-1290 and miR-375 as prognostic markers in castrate resistant prostate cancer

GSE58410 Homo sapiens (human) Non-coding RNA profiling 23 samples Submitted 2014/12/30 Platform GPL11154

At a glance

Non-coding RNA profiling · human · 23 samples

What it is: Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism: Homo sapiens (human)
Topic: Prostate cancerThis series is part of our curated briefing on it.
Samples: 23 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Extracellular microRNAs (miRNAs) embedded in circulating exosomes may serves as prognostic biomarkers in cancer. This study was performed to identify and evaluate plasma exosomal miRNAs for prognostication in castration resistant prostate cancer (CRPC). RNA sequencing was performed to identify candidate exosomal miRNAs associated with overall survival in a screening cohort of 23 CRPC patients.

Read the full summary ↓

Candidate miRNAs were further evaluated for prognosis using qRT-PCR in a follow-up cohort of 100 patients. Cox regression and Kaplan–Meier survival curve analysis were used to evaluate prognostic value of miRNA candidates with and without incorporation of clinical prognostic factors (age, Gleason score and time from androgen deprivation therapy to clinical progression). In the screening cohort, we obtained ~6.80 million mappable RNA reads per patient. Of those with normalized read counts ? 5, 43% were mapped to miRNAs for a total of 375 known and 57 novel miRNAs. Cox regression analysis identified an association of miR-1290, -1246, and -375 with overall survival (FDR<0.1). Of those, higher levels of miR-1290 and -375 were verified to be significantly associated with poor overall survival (p<0.004) in the follow-up cohort. The miR-1290/-375-based prediction model showed better performance with time-dependent area under the curve (AUC) =72% compared to clinical variable-based model with AUC=65%. Plasma exosomal miR-1290 and miR-375 are promising prognostic biomarkers for CRPC patients. Prospective validation is needed for further development of these candidate miRNAs.

This dataset

Open GSE58410 in finder → Find more human datasets → Prostate cancer landscape →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE58410_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

Also filed as BioProject PRJNA252516 and SRA study SRP043122. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 25129854) ↗

Samples in this study

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+ 23 more — browse all 23 samples with per-sample file links →

More Prostate cancer datasets

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GSE222467 The RNA binding proteins LARP4A and LARP4B promote tumour growth and metastasis in prostate cancer and osteosarcoma 12 samples same disease briefing · shares prostate
GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing · shares prostate
GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing
GSE252902 Increased chromatin accessibility drives transition to androgen receptor splice variant dependence in castration-resistant prostate cancer 130 samples shares resistant, prostate
GSE298042 ATAC-Seq of Patient-Derived Xenografts in Metastatic Castration Resistant Prostate Cancer (LuCaP Series) 77 samples shares resistant, prostate

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.