GEO series

Mammalian microRNAs: Experimental evaluation of novel and previously annotated genes

GSE20384 Homo sapiens (human) Non-coding RNA profiling 51 samples Submitted 2010/04/26 Platform GPL9185Platform GPL9052Platform GPL9115

At a glance

Non-coding RNA profiling · human · 51 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)
Samples: 51 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)

MicroRNAs (miRNAs) are small regulatory RNAs that derive from distinctive hairpin transcripts. To learn more about the miRNAs of mammals, we sequenced 60 million small RNAs from mouse brain, ovary, testes, embryonic stem cells, three embryonic stages, and whole newborns. Analysis of these sequences confirmed 387 annotated miRNA genes and identified 110 novel miRNA genes.

Read the full summary ↓

Over 150 previously annotated miRNAs and hundreds of candidates failed to yield sequenced RNAs with miRNA-like features. Ectopically expressing these previously proposed miRNA hairpins also did not yield small RNAs, whereas ectopically expressing the confirmed and newly identified hairpins usually did yield small RNAs with the classical miRNA features, including dependence on the Drosha endonuclease for processing. These experiments, which suggest that previous estimates of conserved mammalian miRNAs were inflated, provide a substantially revised list of confidently identified mammalian miRNAs from which to infer the general features of mammalian miRNAs. Our analyses also revealed new aspects of miRNA biogenesis and modification, including tissue-specific strand preferences, sequential Dicer cleavage of a metazoan pre-miRNA, newly identified instances of miRNA editing, and evidence for widespread Lin28-like miRNA regulation.

This dataset

Open GSE20384 in finder → Find more datasets →

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 GSE20384_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 PRJNA125509 and SRA study SRP002118. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20413612) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 51 more — browse all 51 samples with per-sample file links →

Datasets on a similar topic

GSE61073 mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues 95 samples shares mammalian, micrornas
GSE60426 mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues (sequencing) 85 samples shares mammalian, micrornas
GSE22004 Mammalian microRNAs predominantly act to decrease target mRNA levels 24 samples shares mammalian, micrornas
GSE271926 Evaluation of the Mammalian Aquaporin Inhibitors Auphen and Z433927330 in Treating Breast Cancer 16 samples shares evaluation, mammalian
GSE97179 Single Cell Methylome Signatures Reveal Distinct Neuronal Populations and Regulatory Elements in the Mammalian Cortex 6172 samples shares mammalian
GSE282636 Multiplex generation and single cell analysis of structural variants in mammalian genomes 197 samples shares mammalian
GSE288933 Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers 162 samples shares mammalian
GSE99017 Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation 15 samples shares mammalian

Search all datasets in GEO →

Share this dataset

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.