GEO series

DGCR8 is required for microRNA maturation

GSE6586 Mus musculus (mouse) Non-coding RNA profiling 9 samples Submitted 2007/01/31 Platform GPL4690

At a glance

Non-coding RNA profiling · mouse · 9 samples

What it is: Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism: Mus musculus (mouse)
Samples: 9 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

To determine whether DGCR8 is required for maturation of all miRNAs, we performed miRNA microarray analysis. Using RNA from wild-type ES cells as our reference sample, we observed a global loss of miRNAs in DGCR8 knockout cells, but normal levels of expression in DGCR8 heterozygous cells. The similarity in expression levels between wild-type and heterozygous cells suggests that DGCR8 is not limiting in the maintenance of steady-state levels of miRNAs in ES cells.

Read the full summary ↓

Of the eighty-nine miRNA array probes that showed significant signals with wild-type RNA, eighty-two were drastically reduced in the DGCR8 knockout cells. The remaining seven were not significantly altered in the DGCR8 knockout cells, but at least four of these seven miRNAs appear to be due to unavoidable contamination with RNA from the mouse embryonic fibroblast (MEF) feeder cells used for ES cell culture prior to the isolation of RNA. These miRNAs were highly expressed in the MEFs and decreased when the ES cells were temporarily passaged on gelatin-coated plates without feeders. The remaining three showed similar levels of expression in the heterozygous, knockout and MEF feeder cells. Therefore, these signals may be small RNAs that are not processed with the help of the microprocessor complex. Alternatively, these signals may result from unavoidable degradation products within the purified small RNA population. In either case, our results show that DGCR8 is broadly required for miRNA processing with little evidence for redundancy or bypass mechanisms. Keywords: cell type comparison, genetic modification

This dataset

Open GSE6586 in finder → Find more mouse 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 (GSE6586_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 PRJNA98909. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 17259983) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 9 more — browse all 9 samples with per-sample file links →

Datasets on a similar topic

GSE325932 Disease-associated microRNA, miR-9-2, is required for the timing of retinal progenitor cell competence and the maintenance of Müller glial identity 32 samples shares required, microrna
GSE324933 DGCR8 promotes RNA polymerase II pause release independently of DROSHA [ChIP-seq] 32 samples shares dgcr8
GSE244885 Epididymal acquired sperm microRNAs modify post-fertilization embryonic gene expression 425 samples shares microrna
GSE248181 Maternal SMARCA5 is required for major ZGA in mouse 251 samples shares required
GSE249218 Non-Canonical PRC1.1 is required for the activity of Menin-MLL1 Inhibitors in NUP98-Rearranged AML 220 samples shares required
GSE248180 Maternal SMARCA5 is required for major ZGA in mouse [RNA-seq] 138 samples shares required
GSE281035 PAR3-mediated coordination of hepatocyte proliferation, maturation, and architecture in liver development and regeneration 128 samples shares maturation
GSE293592 Maternal immune activation delays DNA methylation and physiological maturation of cortical excitatory neurons 106 samples shares maturation

Search all mouse datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.