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LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [bulkRNA-seq]

GSE283597 Homo sapiens (human) RNA-seq (gene expression) 45 samples Submitted 2025/06/20 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 45 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
45 samples: 36 distinct titles, 9 of them repeatedGroups 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.
Summary (written by the submitters)
The mechanisms underlying primate-specific genetic programs during early human development remain poorly understood. Long interspersed nuclear element 1 (L1) is the most abundant transposable element in the human genome and represents a vast source of divergent genetic information in hominoid genomes, yet its contribution to human development is largely unknown.
Read the full summary ↓
Using multiomics profiling, we show here that thousands of hominoid-specific L1 loci are expressed in human induced pluripotent stem cells and cerebral organoids. The transcription of unique L1 elements correlates with the absence of DNA methylation and the presence of an active epigenetic state. CRISPRi silencing of L1s revealed the presence of nearly a hundred co-opted L1-derived chimeric transcripts, and silencing of these transcripts results in altered transcription of many genes involved in neural differentiation, leading to a reduction in cerebral organoid size, implicating L1s in hominoid-specific developmental processes. In conclusion, our results show that L1-derived transcripts provide a layer of primate- and human-specific transcriptome complexity that contributes to early human developmental processes.
This dataset
Open GSE283597 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 GSE283597_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 PRJNA1194602 and SRA study SRP549634. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
36 distinct titles, 9 of them repeated
MN07_LacZ_Rep1_bulkRNA_hiPS6_LV3599_L1_CRISPRi ×2 MN07_LacZ_Rep2_bulkRNA_hiPS6_LV3599_L1_CRISPRi ×2 MN07_LacZ_Rep3_bulkRNA_hiPS6_LV3599_L1_CRISPRi ×2 MN07_gRNA1_Rep1_bulkRNA_org_hiPS6_LV3824_L1_C… ×2 MN07_gRNA1_Rep2_bulkRNA_org_hiPS6_LV3824_L1_C… ×2 MN07_gRNA1_Rep3_bulkRNA_org_hiPS6_LV3824_L1_C… ×2 MN07_LacZ_Rep1_bulkRNA_org_hiPS6_LV3599_L1_CR… ×2 MN07_LacZ_Rep2_bulkRNA_org_hiPS6_LV3599_L1_CR… ×2 +1 more

How we read this: Read from 45 sample titles: 36 distinct titles with little repetition. 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

+ 5 more — browse all 45 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.