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Genome-wide Analysis of Class IIa Histone Deacetylase Regulation of Hepatic Gluconeogenesis

GSE20979 Mus musculus (mouse) Expression microarray 16 samples Submitted 2011/09/09 Platform GPL6103
At a glance

Expression microarray · mouse · 16 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Mus musculus (mouse)
Samples
16 samples: 8 conditions, mostly in duplicateGroups 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)
Analysis of Class II Histone Deacetylase (HDAC) regulation of hepatic gluconeogenesis at the gene expression level. We show that in liver, Class IIa HDACs (HDAC4, 5, and 7) are all phosphorylated and excluded from the nucleus by AMPK family kinases. In response to the fasting hormone glucagon, Class IIa HDACs rapidly translocate to the nucleus where they directly bind to the promoters of gluconeogenic enzymes such as G6Pase.
Read the full summary ↓
In turn, HDAC4/5 mediate the acute transcriptional induction of these genes via deacetylation and activation of Foxo family transcription factors. Loss of Class IIa HDACs in the murine liver results in inhibition of FOXO target genes and lowers blood glucose, resulting in increased glycogen storage.
This dataset
Open GSE20979 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 (GSE20979_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 PRJNA124483. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21565617) ↗
Study design
8 conditions, mostly in duplicate
adenoviral GFP DMSO 2h treatment ×2 adenoviral GFP DMSO 4h treatment ×2 adenoviral GFP forskolin 2h treatment ×2 adenoviral GFP forskolin 4h treatment ×2 adenoviral shRNA HDAC4 & 5 DMSO 2h treatment ×2 adenoviral shRNA HDAC4 & 5 DMSO 4h treatment ×2 adenoviral shRNA HDAC4 & 5 forskolin 2h treat… ×2 adenoviral shRNA HDAC4 & 5 forskolin 4h treat… ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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
Datasets on a similar topic

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