Transposable element activity captures human pluripotent cell states [RNA-seq]
RNA-seq (gene expression) · human · 12 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
- 12 samples: 6 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 activity captures human pluripotent cell statesEMBO reports · 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 GSE272117_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 PRJNA1135153 and SRA study SRP519609. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8393469 primed_GFP_1 primed_GFP
- GSM8393470 primed_GFP_RFP_1 primed_GFP_RFP
- GSM8393471 primed_GFP_2 primed_GFP
- GSM8393472 primed_GFP_RFP_2 primed_GFP_RFP
- GSM8393473 Naïve_1 Naïve
- GSM8393474 Naïve_2 Naïve
- GSM8393475 MEKi_1 MEKi
- GSM8393476 MEKi_2 MEKi
- GSM8393477 4CL_GFP_1 4CL_GFP
- GSM8393478 4CL_GFP_RFP_1 4CL_GFP_RFP
- GSM8393479 4CL_GFP_2 4CL_GFP
- GSM8393480 4CL_GFP_RFP_2 4CL_GFP_RFP
- 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
- 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
- GSE275737 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [ChIP-Seq] 21 samples shares transposable, pluripotent, element
- GSE224698 Gene expression profiles of human dermal fibroblasts and human pluripotent stem cells analyzed by bulk RNA-seq 69 samples shares pluripotent, 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
- GSE226477 Bulk RNA-seq of neuromuscular system models generated from human induced pluripotent stem cells (hiPSCs) 15 samples shares pluripotent, rna-seq
- 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.