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Sustained axon regeneration induced by a synergy of PTEN and SOCS3 deletion

GSE32309 Mus musculus (mouse) Expression microarray 12 samples Submitted 2011/10/28 Platform GPL6246

At a glance

Expression microarray · mouse · 12 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Mus musculus (mouse)
Samples: 12 samples: 3 × WT_Crush vs 3 × Pten-KO_Crush vs 3 × Socs3_KO_Crush vs 3 × Double_KO_CrushGroups 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)

A formidable challenge in neural repair in the adult central nervous system (CNS) is the long distances that regenerating axons often need to travel in order to reconnect with their targets. Thus, a sustained capacity for axon regeneration is critical for achieving functional restoration.

Read the full summary ↓

Although deletion of either Phosphatase and tensin homolog (PTEN), a negative regulator of mammalian target of rapamycin (mTOR), or suppressor of cytokine signaling 3 (SOCS3), a negative regulator of Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway, in adult retinal ganglion cells (RGCs) individually promoted significant optic nerve regeneration, such regrowth tapered off around two weeks after the crush injury. Remarkably, we now find that simultaneous deletion of both PTEN and SOCS3 enable robust and sustained axon regeneration. We further show that PTEN and SOCS3 regulate two independent pathways that act synergistically to promote enhanced axon regeneration. Gene expression analyses suggest that double deletion not only result in the induction of many growth-related genes, but also allow RGCs to maintain the expression of a repertoire of genes at the physiological level after injury. Our results reveal concurrent activation of mTOR and STAT3 pathways as a key for sustaining long-distance axon regeneration in adult CNS, a crucial step toward functional recovery.

This dataset

Open GSE32309 in finder → Find more mouse microarray 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 (GSE32309_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 ↓

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 PRJNA147307. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 22056987) ↗

Study design

3 × WT_Crush vs 3 × Pten-KO_Crush vs 3 × Socs3_KO_Crush vs 3 × Double_KO_Crush

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM800486 WT_Crush_Rep_1 WT_Crush
GSM800487 WT_Crush_Rep_2 WT_Crush
GSM800488 WT_Crush_Rep_3 WT_Crush
GSM800489 Pten-KO_Crush_Rep1 Pten-KO_Crush
GSM800490 Pten-KO_Crush_Rep2 Pten-KO_Crush
GSM800491 Pten-KO_Crush_Rep3 Pten-KO_Crush
GSM800492 Socs3_KO_Crush_Rep1 Socs3_KO_Crush
GSM800493 Socs3_KO_Crush_Rep2 Socs3_KO_Crush
GSM800494 Socs3_KO_Crush_Rep3 Socs3_KO_Crush
GSM800495 Double_KO_Crush_Rep1 Double_KO_Crush
GSM800496 Double_KO_Crush_Rep2 Double_KO_Crush
GSM800497 Double_KO_Crush_Rep3 Double_KO_Crush

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