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Transcriptomic profiling of the oocyte-cumulus-granulosa cell complex from estrogen receptor beta knockout mice

GSE268029 Mus musculus (mouse) RNA-seq (gene expression) 93 samples Submitted 2024/10/13 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 93 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
93 samples: 12 conditions, mostly with about 12 replicates eachGroups 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.
Paper
Transcriptomic profiling of the oocyte-cumulus-granulosa cell complex from estrogen receptor β knockout miceF&S science · 2024
Summary (written by the submitters)
Objective: To study the role of estrogen receptor beta in follicle development and maturation and in the response to gonadotropin stimulation aiming at superovulation. Animals: Healthy wild-type and estrogen receptor beta (ERβ) knockout female mice aged 4 weeks, 7 weeks, and 6 months. analysis. Main Outcomes: Oocyte yield after superovulation, transcriptomic profiling of cumulus cells and oocytes and immunohistochemical analyses.
Read the full summary ↓
Results: Superovulation of ERβ knockout (Esr2-KO) mice results in reduced oocyte yield at 6-months of age compared to wild-type (WT) mice. RNA-seq analysis of cumulus cells from superovulated WT and Esr2-KO mice identified genes and pathways associated with among others adhesion, proliferation, Wnt-signaling, and placed ERβ in bipotential granulosa cell cluster. Loss of ERβ increased expression of the other estrogen receptors Esr1 and Gper1. Conclusion: Our results show that ERβ has an important role in regulating ovulation in response to exogenous gonadotropins in 6-month-old mice, but not in younger mice. Our transcriptomic and immunohistochemical observations suggest a dysregulation of the granulosa cell communication and lack of tight coordination between granulosa cell replication and antrum expansion. A significant upregulation of other estrogen receptors supports a compensatory mechanism sustaining fertility during younger age in Esr2-KO mice.
Published in
Transcriptomic profiling of the oocyte-cumulus-granulosa cell complex from estrogen receptor β knockout mice
Töhönen V, Antonson P, Boggavarapu NR et al. · F&S science 2024 · PMID 39168303 · doi:10.1016/j.xfss.2024.08.004
This dataset
Open GSE268029 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 GSE268029_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 PRJNA1114073 and SRA study SRP508980. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39168303) ↗
Study design
12 conditions, mostly with about 12 replicates each
Granulosa cells from wild type mice-6month-Sa… ×12 oocytes from wild type mice-week4-sample ×12 oocytes from knock-out mice-week7-sample ×12 oocytes from wild type mice-6month-sample ×11 Granulosa cells from wild type mice-Week4-Sam… ×7 Granulosa cells from knock-out mice-Week4-Sam… ×7 oocytes from knock-out mice-week4-sample ×7 Granulosa cells from knock-out mice-6month-Sa… ×6 +4 more

Supports a between-group comparison across 93 samples.

How we read this: 12 replicated groups read from 93 sample titles; they account for 93 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

+ 53 more — browse all 93 samples with per-sample file links →

Datasets on a similar topic

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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.