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Global analyses of RNA G-quadruplexes

GSE83617 Pseudomonas putida; Saccharomyces cerevisiae; Homo sapiens; Escherichia coli; Mus musculus; Parasynechococcus marenigrum WH 8102 Other 35 samples Submitted 2016/09/24 Platform GPL19659Platform GPL14548Platform GPL21126Platform GPL13821Platform GPL13112Platform GPL11154
At a glance

Pseudomonas putida; Saccharomyces cerevisiae; Homo sapiens; Escherichia coli; Mus musculus; Parasynechococcus marenigrum WH 8102 · 35 samples

Organism
Pseudomonas putida; Saccharomyces cerevisiae; Homo sapiens; Escherichia coli; Mus musculus; Parasynechococcus marenigrum WH 8102
Samples
35 samples: 28 distinct titles, 7 of them repeatedGroups 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)
In vitro, some RNAs can form stable four-stranded structures known as G-quadruplexes. Although RNA G-quadruplex structures have been implicated in post-transcriptional gene regulation and diseases, direct evidence for quadruplex formation in cells has been lacking. Here, we developed a suite of methods that identify RNAs with quadruplex-forming ability and measure their folding state in living cells. Applying these methods to mammalian cell lines, the budding yeast S. cerevisiae and several bacteria, we characterized the folding landscapes of RNA G-quadruplexes in these species.
This dataset
Open GSE83617 in finder → Find more datasets →
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 (GSE83617_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 PRJNA326510 and SRA study SRP076921. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 27708011) ↗
Study design
28 distinct titles, 7 of them repeated
mESC_DMS_vitro_K ×2 mESC_DMS_vivo ×2 Yeast_DMS_vitro_K ×2 Ecoli_DMS_vitro_K ×2 Pputida_DMS_vitro_K ×2 Synechococcus_DMS_vitro_K ×2 mESC_NAI_vitro_K ×2

How we read this: Read from 35 sample titles: 28 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
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