GEO series

m6A in 5’ untranslated regions promotes cap-independent translation of mRNA

GSE73405 Homo sapiens (human) Other 7 samples Submitted 2015/10/26 Platform GPL16791Platform GPL11154

At a glance

human · 7 samples

Organism: Homo sapiens (human)
Samples: 7 samples: 2 × eif3a_par-iclip vs 2 × HepG2 Heat Shock vs 2 × HepG2 ControlGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

N6-methyladenosine (m6A) is a widespread internal RNA modification whose function is poorly understood. Here we report that m6A residues within the 5'UTR promote a novel form of cap-independent translation which is mediated through an interaction between m6A residues and the translation initiation factor, eIF3. We performed m6A profiling in cells subjected to heat shock stress and observed increased 5'UTR methylation after heat shock.

Read the full summary ↓

For these studies, we used single-nucleotide resolution m6A mapping (miCLIP), which enables the detection of m6A residues separately from m6Am residues. Thus, the goal of these experiments was to identify m6A residues which are increased in the 5'UTR after heat shock stress.

This dataset

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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE73405_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA296900 and SRA study SRP064176. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26593424) ↗

Study design

2 × eif3a_par-iclip vs 2 × HepG2 Heat Shock vs 2 × HepG2 Control

Supports a between-group comparison across 6 samples.

How we read this: 3 replicated groups read from 7 sample titles; they account for 6 of them. 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

GSM1892896 eif3a_par-iclip_replicate1 eif3a_par-iclip
GSM1892897 eif3a_par-iclip_replicate2 eif3a_par-iclip
GSM2011452 HEK Heat Shock 1
GSM2011453 HepG2 Heat Shock 1 HepG2 Heat Shock
GSM2011454 HepG2 Heat Shock 2 HepG2 Heat Shock
GSM2011455 HepG2 Control 1 HepG2 Control
GSM2011456 HepG2 Control 2 HepG2 Control

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