GEO series

Human stem cells with in vivo high plasticity generated by cell-cell communication

GSE242346 Homo sapiens (human) RNA-seq (gene expression) 22 samples Submitted 2025/02/07 Platform GPL20301Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 22 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: Homo sapiens (human)
Samples: 22 samples: 8 conditions, mostly in triplicateGroups 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: Human stem cells with in vivo high plasticity generated by cell-cell communicationProceedings of the National Academy of Sciences of the United States of America · 2025

Summary (written by the submitters)

We report the discovery of a population of tiny, dormant cells from human peripheral blood, which upon activation and maturation in vitro exhibit unique transcriptome and cellular phenotypes, distinct from all known cell types.

Read the full summary ↓

These novel cells can deliver RNA-rich granules to suitable recipient cells and provide guidance, and are thus named “mature Guide Cells” (or m-GCs) and their dormant precursors are named “pre-GCs.” When m-GCs are co-cultured with human umbilical cord-derived mesenchymal stromal cells (UC-MSCs), cell-cell communication occurs in which RNA-rich granules are transferred from m-GCs to UC-MSCs via tunneling nanotubes (TNT). As a result, a novel type of stem cells with high plasticity is generated, which can be induced to differentiate into the representative cell types from all three germ layers in vitro. The newly generated stem cells, named “guide integrated adult Stem Cells” (or giaSCs) are characterized by unique cell morphology, gene expression, and phenotypic profile. They are also observed to have a remarkable capacity to promote tissue reconstitution in vivo.

Published in

Human stem cells with in vivo high plasticity generated by cell-cell communication

Li S, Chen X, Xin J et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40067886 · doi:10.1073/pnas.2413043122

This dataset

Open GSE242346 in finder → Find more human 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 GSE242346_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 PRJNA1013372 and SRA study SRP458939. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40067886) ↗

Study design

8 conditions, mostly in triplicate

pre-GC, individual 1, ×3 pre-GC, individual 2, ×3 m-GC, individual 3, ×3 m-GC, individual 4, ×3 giaSC, mGC from individual 5, UC-MSC from per… ×3 giaSC, mGC from individual 6, UC-MSC from per… ×2 UC-MSC, person 1, ×2 UC-MSC, person 2, ×2 +1 more

Supports a between-group comparison across 21 samples.

How we read this: 8 replicated groups read from 22 sample titles; they account for 21 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

GSM7759630 pre-GC, individual 1, replicate 1 pre-GC, individual 1,
GSM7759631 pre-GC, individual 1, replicate 2 pre-GC, individual 1,
GSM7759632 pre-GC, individual 1, replicate 3 pre-GC, individual 1,
GSM7759633 pre-GC, individual 2, replicate 1 pre-GC, individual 2,
GSM7759634 pre-GC, individual 2, replicate 2 pre-GC, individual 2,
GSM7759635 pre-GC, individual 2, replicate 3 pre-GC, individual 2,
GSM7759636 m-GC, individual 3, replicate 1 m-GC, individual 3,
GSM7759637 m-GC, individual 3, replicate 2 m-GC, individual 3,
GSM7759638 m-GC, individual 3, replicate 3 m-GC, individual 3,
GSM7759639 m-GC, individual 4, replicate 1 m-GC, individual 4,
GSM7759640 m-GC, individual 4, replicate 2 m-GC, individual 4,
GSM7759641 m-GC, individual 4, replicate 3 m-GC, individual 4,
GSM7759642 giaSC, mGC from individual 5, UC-MSC from person 1, passage 3, replicate 1 giaSC, mGC from individ…
GSM7759643 giaSC, mGC from individual 5, UC-MSC from person 1, passage 3, replicate 2 giaSC, mGC from individ…
GSM7759644 giaSC, mGC from individual 5, UC-MSC from person 1, passage 3, replicate 3 giaSC, mGC from individ…
GSM7759645 giaSC, mGC from individual 6, UC-MSC from person 1, passage 7, replicate 1 giaSC, mGC from individ…
GSM7759646 giaSC, mGC from individual 6, UC-MSC from person 1, passage 7, replicate 2 giaSC, mGC from individ…
GSM7759647 UC-MSC, person 1, replicate 1 UC-MSC, person 1,
GSM7759648 UC-MSC, person 1, replicate 2 UC-MSC, person 1,
GSM7759649 UC-MSC, person 2, replicate 1 UC-MSC, person 2,
GSM7759650 UC-MSC, person 2, replicate 2 UC-MSC, person 2,
GSM7759651 m-GC, scRNAseq

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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.