Systematic analyses of transposable element expression dynamics using long read RNA-seq in pluripotent stem cells and germ lineage cells [bulk RNA-seq]
RNA-seq (gene expression) · human · 16 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
- 16 samples: 7 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
- Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineagesNature communications · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE269273_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1120863 and SRA study SRP512259. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 7 replicated groups read from 16 sample titles; they account for 16 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.
- GSM8312179 Bulk RNA-seq Ectoderm Repeat 1 Bulk RNA-seq Ectoderm R…
- GSM8312180 Bulk RNA-seq Ectoderm Repeat 2 Bulk RNA-seq Ectoderm R…
- GSM8312181 Bulk RNA-seq Endoderm Repeat 1 Bulk RNA-seq Endoderm R…
- GSM8312182 Bulk RNA-seq Endoderm Repeat 2 Bulk RNA-seq Endoderm R…
- GSM8312183 Bulk RNA-seq Endoderm Repeat 3 Bulk RNA-seq Endoderm R…
- GSM8312184 Bulk RNA-seq hPSC Repeat 1 Bulk RNA-seq hPSC Repeat
- GSM8312185 Bulk RNA-seq hPSC Repeat 2 Bulk RNA-seq hPSC Repeat
- GSM8312186 Bulk RNA-seq hPSC Repeat 3 Bulk RNA-seq hPSC Repeat
- GSM8312187 Bulk RNA-seq Mesoderm Repeat 1 Bulk RNA-seq Mesoderm R…
- GSM8312188 Bulk RNA-seq Mesoderm Repeat 2 Bulk RNA-seq Mesoderm R…
- GSM9038155 Bulk RNA-seq hESF treated with endoderm-inducing medium Repeat 1 Bulk RNA-seq hESF treat…
- GSM9038156 Bulk RNA-seq hESF treated with endoderm-inducing medium Repeat 2 Bulk RNA-seq hESF treat…
- GSM9038157 Bulk RNA-seq hESF treated with mesoderm-inducing medium Repeat 1 Bulk RNA-seq hESF treat…
- GSM9038158 Bulk RNA-seq hESF treated with mesoderm-inducing medium Repeat 2 Bulk RNA-seq hESF treat…
- GSM9038159 Bulk RNA-seq hESF untreated Repeat 1 Bulk RNA-seq hESF untre…
- GSM9038160 Bulk RNA-seq hESF untreated Repeat 2 Bulk RNA-seq hESF untre…
- GSE274217 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [RNA-Seq] 28 samples shares transposable, pluripotent, element, rna-seq
- GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares dynamics, rna-seq, long
- GSE283597 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [bulkRNA-seq] 45 samples shares transposable, element, rna-seq
- GSE261306 Early Prediction of Preeclampsia Based on Transposable Elements Deregulation in the Placenta [RNA-Seq] 30 samples shares transposable, element, rna-seq
- GSE285570 Transcriptional regulation of temporal dynamics in human neurogenesis and neuronal maturation [RNA-seq] 50 samples shares dynamics, rna-seq
- GSE342790 Development-inspired approach for the derivation of functional and transplantable salivary gland organoids from human pluripotent stem cells [RNA-Seq] 16 samples shares pluripotent, rna-seq
- GSE228382 Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer. 16 samples shares dynamics, lineage
- GSE287227 Transient SP140 inhibition unlocks hematopoietic stem cell fate from human pluripotent stem cells [scRNA-seq] 9 samples shares pluripotent, rna-seq
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.