GEO series

RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [polyA_RNA-seq-Nu_Cy]

GSE247849 Mus musculus (mouse) RNA-seq (gene expression) 13 samples Submitted 2024/09/09 Platform GPL21273

At a glance

RNA-seq (gene expression) · mouse · 13 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 13 samples: 6 conditions, mostly in duplicateGroups 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; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Exosome is the main RNA surveillance and degradation pathway during oocyte growth. To figure out specific roles of RNA surveillance in oocyte growth, the pathway was destroied by deleting MTR4, the only known RNA helicase in exosome pathway. Poly(A) RNA-seq was performed using samples after nucleus-cytoplasm separation to examine the global subcellular transcriptional changes.

This dataset

Open GSE247849 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE247849_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1017097 and SRA study SRP460355. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in duplicate

Day-21-WT-Nucleus ×3 Day-14-WT-Nucleus ×2 Day-14-WT-Cytoplasm ×2 Day-21-WT-Cytoplasm ×2 Day-21-MTR4-null-Nucleus ×2 Day-21-MTR4-null-Cytoplasm ×2

Supports a between-group comparison across 13 samples.

How we read this: 6 replicated groups read from 13 sample titles; they account for 13 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

GSM7901511 Day-14-WT-Nucleus-rep1 Day-14-WT-Nucleus
GSM7901512 Day-14-WT-Nucleus-rep2 Day-14-WT-Nucleus
GSM7901513 Day-14-WT-Cytoplasm-rep1 Day-14-WT-Cytoplasm
GSM7901514 Day-14-WT-Cytoplasm-rep2 Day-14-WT-Cytoplasm
GSM7901515 Day-21-WT-Nucleus-rep1 Day-21-WT-Nucleus
GSM7901516 Day-21-WT-Nucleus-rep2 Day-21-WT-Nucleus
GSM7901517 Day-21-WT-Nucleus-rep3 Day-21-WT-Nucleus
GSM7901518 Day-21-WT-Cytoplasm-rep1 Day-21-WT-Cytoplasm
GSM7901519 Day-21-WT-Cytoplasm-rep2 Day-21-WT-Cytoplasm
GSM7901520 Day-21-MTR4-null-Nucleus-rep1 Day-21-MTR4-null-Nucleus
GSM7901521 Day-21-MTR4-null-Nucleus-rep2 Day-21-MTR4-null-Nucleus
GSM7901522 Day-21-MTR4-null-Cytoplasm-rep1 Day-21-MTR4-null-Cytopl…
GSM7901523 Day-21-MTR4-null-Cytoplasm-rep2 Day-21-MTR4-null-Cytopl…

Datasets on a similar topic

GSE262431 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [day 14 total_RNA-seq-Nu_Cy] 12 samples shares mtr4, surveillance, determines, rna-seq-nu, helicase, oocytes, volume
GSE247848 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [polyA_RNA-seq] 12 samples shares mtr4, surveillance, determines, helicase, oocytes, volume, polya
GSE247850 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [total_RNA-seq-Nu_Cy] 9 samples shares mtr4, surveillance, determines, rna-seq-nu, helicase, oocytes, volume
GSE247852 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes 54 samples shares mtr4, surveillance, determines, helicase, oocytes, volume
GSE271546 The expression order determines the pioneer functions of Ngn3 and NeuroD1 in pancreatic endocrine differentiation -2 447 samples shares determines
GSE278182 Genetic background and oncogenic driver determines the genomic evolution and transcriptomics of mammary tumor metastasis 74 samples shares determines
GSE263021 TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states [RNA-seq - matched healthy and tumor tissues] 41 samples shares determines
GSE244344 Activated-ATF6α is an ER stress-inducing oncoprotein metabolically restricting immunosurveillance 38 samples shares surveillance

Search all mouse RNA-seq 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.