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Uterine epithelial ERα regulates preimplantation uterine luminal epithelial (LE) and uterine mRNAs

GSE311705 Mus musculus (mouse) RNA-seq (gene expression) 59 samples Submitted 2025/12/01 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 59 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
59 samples: 12 conditions, mostly with about 4 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
Uterine epithelial estrogen receptor α temporally regulates preimplantation uterine immunity involving interleukin-1β signalingReproductive and developmental medicine · 2026
Summary (written by the submitters)
Uterine epithelial estrogen receptor α (ERα) deficiency in epiERα-/- (Esr1f/-Wnt7aCre/+) mice leads to dysregulated environment of uterine lumen, which is lined by uterine luminal epithelium (LE). We hypothesized that LE transcriptomes held molecular keys to understanding ERα in regulating preimplantation uterine environment. Day 0.5 post-coitum (D0.5) and D3.5 LE (isolated via enzymatic digestion), digested uterus (DU), and flash-frozen uterus (U) from Esr1f/- (control) and epiERα-/- mice were processed for mRNA-seq.
Read the full summary ↓
There were minimal differentially expressed genes (DEGs, TPM>1, FC>2, FDR<0.05) between DU and U. Between D0.5 and D3.5 Esr1f/- LE, the top upregulated and downregulated GOBP pathways were on cellular processes and on innate immune responses, respectively, with the later also seen in Esr1f/- U. Compared to Esr1f/- LE, the most upregulated and downregulated pathways in D0.5 epiERα-/- LE were on innate immune responses and on biosynthesis and metabolism, respectively; while those in D3.5 epiERα-/- LE were on cell division and on signaling and metabolic processes, respectively. Na+ transmembrane transport was among shared upregulated pathways in D0.5 and D3.5 epiERα-/- LE. Between Esr1f/- and epiERα-/-, most DEGs in U were also DEGs in LE, limited DEGs in U only with higher expression than in LE were related to immune responses, implicating potential paracrine effects of uterine epithelial ERα. Selected DEGs were verified by realtime PCR and immunohistochemistry. This mRNA-seq dataset provides molecular keys to understanding temporal (e.g., innate immunity) and constituent (e.g., uterine fluid movement) functions, and potential paracrine effects of uterine epithelial ERα in regulating the preimplantation uterine environment.
Published in
Uterine epithelial estrogen receptor α temporally regulates preimplantation uterine immunity involving interleukin-1β signaling
Hancock JM, Martin TE, Li Y et al. · Reproductive and developmental medicine 2026 · PMID 41710727 · doi:10.1097/RD9.0000000000000149
This dataset
Open GSE311705 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 GSE311705_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 PRJNA1370275 and SRA study SRP649450. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41710727) ↗
Study design
12 conditions, mostly with about 4 replicates each
D0.5 Esr1f/- Control Luminal Epithelium ×9 D0.5 epiERa-/- Knockout Luminal Epithelium ×7 D3.5 epiERa-/- Knockout Luminal Epithelium ×6 D0.5 Esr1f/- Control Uterus ×6 D3.5 Esr1f/- Control Uterus ×5 D3.5 epiERa-/- Knockout Uterus ×5 D3.5 Esr1f/- Control Luminal Epithelium ×4 D0.5 epiERa-/- Knockout Uterus ×4 +4 more

Supports a case/control comparison: 28 samples read as cases, 31 as controls.

How we read this: 12 replicated groups read from 59 sample titles; they account for 59 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

+ 19 more — browse all 59 samples with per-sample file links →

Datasets on a similar topic

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