GEO series

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

GSE247848 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/09/09 Platform GPL21273

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 3 × WT-Day-14 vs 3 × WT-Day-21 vs 3 × MTR4-Day-14 vs 3 × MTR4-Day-21Groups 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 to examine the global transcriptional changes.

This dataset

Open GSE247848 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 GSE247848_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 PRJNA1015136 and SRA study SRP459606. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × WT-Day-14 vs 3 × WT-Day-21 vs 3 × MTR4-Day-14 vs 3 × MTR4-Day-21

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

GSM7901499 WT-Day-14_rep1 WT-Day-14
GSM7901500 WT-Day-14_rep2 WT-Day-14
GSM7901501 WT-Day-14_rep3 WT-Day-14
GSM7901502 WT-Day-21-rep1 WT-Day-21
GSM7901503 WT-Day-21-rep2 WT-Day-21
GSM7901504 WT-Day-21-rep3 WT-Day-21
GSM7901505 MTR4-Day-14-rep1 MTR4-Day-14
GSM7901506 MTR4-Day-14-rep2 MTR4-Day-14
GSM7901507 MTR4-Day-14-rep3 MTR4-Day-14
GSM7901508 MTR4-Day-21-rep1 MTR4-Day-21
GSM7901509 MTR4-Day-21-rep2 MTR4-Day-21
GSM7901510 MTR4-Day-21-rep3 MTR4-Day-21

Datasets on a similar topic

GSE247849 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [polyA_RNA-seq-Nu_Cy] 13 samples shares mtr4, surveillance, determines, helicase, oocytes, rna-seq, volume, polya
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, helicase, oocytes, rna-seq, volume
GSE247850 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [total_RNA-seq-Nu_Cy] 9 samples shares mtr4, surveillance, determines, helicase, oocytes, rna-seq, volume
GSE247852 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes 54 samples shares mtr4, surveillance, determines, helicase, oocytes, volume
GSE263021 TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states [RNA-seq - matched healthy and tumor tissues] 41 samples shares determines, rna-seq
GSE306744 Pre-division TCF1 downregulation determines long-term effector and memory CD8 T cell fates [RNA-Seq] 31 samples shares determines, rna-seq
GSE277903 Innate tissue immunosurveillance by γδ T cells has real-time dependence on the T cell receptor [RNA-seq] 23 samples shares surveillance, rna-seq
GSE270640 Dnmt1 determines bone length by regulating energy metabolism of growth plate chondrocytes [RNA-seq] 22 samples shares determines, rna-seq

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