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Essential lncRNAs in the human transcriptome

GSE326230 Homo sapiens (human) Single-cell RNA-seq 30 samples Submitted 2026/04/01 Platform GPL18573
At a glance

Single-cell RNA-seq · human · 30 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
30 samples: 15 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
Essential lncRNAs in the human transcriptomeCell genomics · 2026
Summary (written by the submitters)
Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using RNA-targeting CRISPR-Cas13 screens, we probed how loss of ~5,500 lncRNAs impacts cell fitness across five human cell lines and identified 788 lncRNAs with context-specific or broad essentiality.
Read the full summary ↓
We confirm their essentiality with individual perturbations and find that the majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that loss of essential lncRNAs impair cell cycle progression and drive apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development. Using ~9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13.
Published in
Essential lncRNAs in the human transcriptome
Liang WW, Mueller SJ, Hart SK et al. · Cell genomics 2026 · PMID 42155443 · doi:10.1016/j.xgen.2026.101253
This dataset
Open GSE326230 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 GSE326230_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 PRJNA1161603 and SRA study SRP543663. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42155443) ↗
Study design
15 conditions, mostly in duplicate
RfxCas13d expressing HAP1 cells, pooled lncRN… ×2 RfxCas13d expressing HAP1 cells, pooled lncRN… ×2 RfxCas13d expressing HAP1 cells, pooled lncRN… ×2 RfxCas13d expressing HEK293FT cells, pooled l… ×2 RfxCas13d expressing HEK293FT cells, pooled l… ×2 RfxCas13d expressing HEK293FT cells, pooled l… ×2 RfxCas13d expressing K562 cells, pooled lncRN… ×2 RfxCas13d expressing K562 cells, pooled lncRN… ×2 +7 more

Supports a between-group comparison across 30 samples.

How we read this: 15 replicated groups read from 30 sample titles; they account for 30 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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