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LRP1high subpopulation of human umbilical cord mesenchymal stem cell (hUC-MSC)transplantationimproves ovarian function in POF and aging mice

GSE239500 Mus musculus (mouse) Single-cell RNA-seq 21 samples Submitted 2024/03/13 Platform GPL17021
At a glance

Single-cell RNA-seq · mouse · 21 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
21 samples: 8 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.
Paper
Transplantation of the LRP1(high) subpopulation of human umbilical cord-derived mesenchymal stem cells improves ovarian function in mice with premature ovarian failure and aged miceStem cell research & therapy · 2024
Summary (written by the submitters)
This study revealed the heterogeneity of UC-MSCs using single-cell sequencing technology (10x Genomics). Through in vitro and in vivo experiments, it was determined that the LRP1high UC-MSCs subpopulation has therapeutic effects in improving ovarian function. This finding provides theoretical support for the screening of stem cell preparations for use in POF, aiming to reduce the impact of other interfering cell components on ovarian tissue and provide precise, safe, and effective clinical strategies for stem cell therapy in POF.
Read the full summary ↓
Mechanistic exploration further revealed that the LRP1high UC-MSCs subpopulation primarily improves mitochondrial function of granulosa cells by modulating DNA damage pathways, extracellular matrix-related signals, and cellular metabolism. Consequently, it more effectively enhances the quality of aging mouse oocytes, offering new insights into targeting LRP1high UC-MSCs for precise treatment of premature ovarian failure.
Published in
Transplantation of the LRP1(high) subpopulation of human umbilical cord-derived mesenchymal stem cells improves ovarian function in mice with premature ovarian failure and aged mice
Shen J, Wu L, Shi X et al. · Stem cell research & therapy 2024 · PMID 38438896 · doi:10.1186/s13287-024-03660-0
This dataset
Open GSE239500 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 GSE239500_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA999596 and SRA study SRP451947. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38438896) ↗
Study design
8 conditions, mostly in duplicate
oocyte_young.biol ×3 oocyte_old+lrp1high.biol ×3 granulosa_old+lrp1high.biol ×3 oocyte_old.biol ×2 oocyte_old+all.biol ×2 oocyte_old+lrp1low.biol ×2 granulosa_old.biol ×2 granulosa_old+lrp1low.biol ×2 +2 more

Supports a between-group comparison across 19 samples.

How we read this: 8 replicated groups read from 21 sample titles; they account for 19 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
Datasets on a similar topic

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