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tRNA-overlapping long non-coding RNAs loci repress codon-biased genes

GSE273784 Homo sapiens (human) RNA-seq (gene expression) 47 samples Submitted 2025/08/22 Platform GPL20301Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 47 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
47 samples: 11 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.
Summary (written by the submitters)
The functions of most long non-coding RNAs (lncRNAs) are not known. Here, we define a group of ‘tRNA-Overlapping LncRNA’ (tROL) genes that are upregulated during in vitro cartilage development. Deletions of tROLs result in changes in the expression of codon-biased genes, where downregulated genes are enriched in codons corresponding to tRNAs overlapping disrupted tROLs.
Read the full summary ↓
tROL loci are located in gene-dense regions and interact extensively between chromosomes, and tROL whole-gene deletions result in the upregulation of significantly overlapping subsets of genes in the vicinity of tROL loci. Inhibiting the lncRNA transcription and degrading the lncRNA transcripts of a tROL gene downregulates tRNA expression. Taken together, the results suggest that tROL loci coalesce and are dependent on each other’s transcription to repress genes in spatial proximity and to activate tRNA expression. Our investigation thus provides insight into a previously uncharacterized role for tROLs as a regulatory bridge between the non-coding and coding genomes.
This dataset
Open GSE273784 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 GSE273784_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 PRJNA1143053 and SRA study SRP523719. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
11 conditions, mostly in duplicate
C-28/I2 chondrocytes, WT, clone 1, passage ×3 C-28/I2 chondrocytes, LINC00324 KO, clone 1, … ×3 HEK-293 cells, WT, clone 1, passage ×3 HEK-293 cells, LINC00324 KO, clone 1, passage ×3 C-28/I2 chondrocytes, LINC00324 KO, clone 2, … ×2 HEK-293 cells, LINC00324 KO, clone 2, passage ×2 HEK-293 cells, LINC01962 KO, clone ×2 HEK-293 cells, ENSG00000284607 KO, clone ×2 +24 more

Supports a between-group comparison across 26 samples.

How we read this: 11 replicated groups read from 47 sample titles; they account for 26 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

+ 7 more — browse all 47 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.