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Gene expression RNAseq profiles of TNKS/PARP-inhibitor Regulated Naïve (TIRN) cells with or without transgenic inducible DUX4 (iDUX4) activation.

GSE271242 Homo sapiens (human) Single-cell RNA-seq 21 samples Submitted 2025/05/12 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 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
Homo sapiens (human)
Samples
21 samples: 7 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
Proteogenomic reprogramming to a functional human blastomere-like stem cell state via a PARP-DUX4 regulatory axisCell reports · 2025
Summary (written by the submitters)
Proteogenomic Reprogramming to a Functional Human Blastomere-like Stem Cell State via a PARP-DUX4 Regulatory Axis; Zimmerlin et al, 2024. PARP1 (ARTD1) and Tankyrases (TNKS1/TNKS2; PARP5a/5b) are poly-ADP-ribose polymerases (PARPs) with catalytic and non-catalytic functions that regulate both the genome and proteome during zygotic genome activation (ZGA), totipotent, and pluripotent embryonic stages.
Read the full summary ↓
Here, we show that primed, conventional human pluripotent stem cells (hPSC) cultured continuously under non-specific TNKS1/TNKS2/PARP1-inhibited chemical naïve reversion conditions underwent epigenetic reprogramming to clonal blastomere-like stem cells. TIRN stem cells concurrently expressed hundreds of gene targets of the ZGA-priming pioneer factor DUX4, as well as a panoply of four-cell (4C)-specific (e.g., TPRXL, HOX clusters), eight-cell (8C)-specific (e.g., DUXA, GSC, GATA6), primitive endoderm-specific (e.g., GATA4, SOX17), trophectoderm-specific (e.g., CDX2, TFAP2C), and naïve epiblast-specific (e.g., DNMT3L, NANOG, POU5F1(OCT4)) factors; all in a hybrid, combinatorial single-cell manner. Mapping of proteomic and single-cell expressions of TIRN cells against human preimplantation embryo references identified them as relatively homogenous 4C-8C stage populations. The bulk RNA-seq and proteomics analyses of TIRN cells (+/- iDUX4) revealed acquisition of pre-lineage embryonic transcriptional programs. To determine if TIRN +/- iDUX4 cells were mixed populations or clonal blastomere-like cells, single cell (sc)RNA-seq was performed to investigate transcriptional heterogeneity at a single cell level. Overall, single, unmodified TIRN cells shared high transcriptional identity with single TIRN+iDUX4 cells, and single primed hPSC and TIRN +/- iDUX4 cells expressed comparable and uniformly homogenous levels of core pluripotency factors (e.g., NANOG, POU5F1 (OCT4), SOX2, KLF4, CMYC). However, single TIRN and TIRN+iDUX4 populations homogenously co-expressed not only higher levels of naïve ICM-specific genes (e.g., DNMT3L, SP5, ERVH48-1, GDF3, and IFITM1) (Park et al., 2020; Zimmerlin et al., 2016), but also hundreds of diverse and antagonistic lineage-specifying genes (e.g., HOX-PRD, T-BOX, FOX, GATA families) that are co-expressed simultaneously only during 4C-to-morula human embryonic stages (Petropoulos et al., 2016; Zou et al., 2022). Transcript levels of 4C-specific (i.e., TPRXL, HOXA1, EBF2), 8C-specific (i.e., GATA6, FOXB1), trophectoderm lineage-specific (i.e., CDX2, TFAP2C), and endoderm lineage-specific (i.e., GATA4, SOX17) pioneer factors were co-expressed in the same single cell populations; with expressions that were further augmented following iDUX4 activation.
Published in
Proteogenomic reprogramming to a functional human blastomere-like stem cell state via a PARP-DUX4 regulatory axis
Zimmerlin L, Angarita A, Park TS et al. · Cell reports 2025 · PMID 40338744 · doi:10.1016/j.celrep.2025.115671
This dataset
Open GSE271242 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 GSE271242_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 PRJNA1130513 and SRA study SRP517349. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40338744) ↗
Study design
7 conditions, mostly in triplicate
RUES02, primed (E8), RNAseq, batch 01, ×3 RUES02, TIRN (LIF-3i), RNAseq, batch 01, ×3 RUES02, TIRN+iDUX4 (LIF-3i + dox), RNAseq, ba… ×3 RUES02, primed (E8), RNAseq, batch 02, ×3 RUES02, primed+iDUX4 (E8 + dox), RNAseq, batc… ×3 RUES02, TIRN (LIF-3i), RNAseq, batch 02, ×3 RUES02, TIRN+iDUX4 (LIF-3i + dox), RNAseq, ba… ×3

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 21 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
Datasets on a similar topic

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