GEO series

Mammalian microRNAs predominantly act to decrease target mRNA levels

GSE22004 Homo sapiens (human) Expression microarray 24 samples Submitted 2010/08/03 Platform GPL9115Platform GPL570Platform GPL9250Platform GPL1261

At a glance

Expression microarray · human · 24 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels.

Read the full summary ↓

Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output. This SuperSeries is composed of the SubSeries listed below.

This dataset

Open GSE22004 in finder → Find more RNA-seq 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 GSE22004_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 ↗

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA127467 and SRA study SRP002605. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20703300) ↗

Study design

24 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 3 samples read as cases, 9 as controls.

How we read this: Read from 24 sample titles: 24 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM546920 Footprint_mock_32hr_runs1-2
GSM546921 mRNASeq_mock_32hr_runs1-3
GSM546922 Footprint_miR-155_32hr_runs1-2
GSM546923 mRNASeq_miR-155_32hr_runs1-3
GSM546924 Footprint_miR-1_32hr_runs1-2
GSM546925 mRNASeq_miR-1_32hr_runs1-3
GSM546926 Footprint_mock_12hr_run1
GSM546927 mRNASeq_mock_12hr_runs1-2
GSM546928 Footprint_miR-155_12hr_run1
GSM546929 mRNASeq_miR-155_12hr_runs1-2
GSM546930 Footprint_miR-1_12hr_run1
GSM546931 mRNASeq_miR-1_12hr_runs1-2
GSM546987 Footprint_wild-type_runs1-2
GSM546988 mRNASeq_wild-type_runs1-3
GSM546989 Footprint_mir-223-knockout_runs1-2
GSM546990 mRNASeq_mir-223-knockout_runs1-3
GSM546991 HeLa cells, mock-transfected, 32hr
GSM546992 HeLa cells, transfected with miR-155 duplex, 32hr
GSM546993 HeLa cells, transfected with miR-1 duplex, 32hr
GSM546994 HeLa cells, mock-transfected, 12hr
GSM546995 HeLa cells, transfected with miR-155 duplex, 12hr
GSM546996 HeLa cells, transfected with miR-1 duplex, 12hr
GSM546997 Neutrophils cultured from wild-type mouse bone marrow
GSM546998 Neutrophils cultured from mir-223 knockout mouse bone marrow

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