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Essential lncRNAs in the human transcriptome [CRISPR]

GSE326978 Homo sapiens (human) Single-cell RNA-seq 16 samples Submitted 2026/04/06 Platform GPL34281
At a glance

Single-cell RNA-seq · human · 16 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
16 samples: 4 × RfxCas13d expressing HAP1 cells, bcgRNA-derived cDNA 10x vs 4 × RfxCas13d expressing HAP1 cells, mRNA-derived cDNA 10x vs 4 × RfxCas13d expressing MDA-MB-231 cells, bcgRNA-derived cDNA 10x vs 4 × RfxCas13d expressing MDA-MB-231 cells, mRNA-derived cDNA 10xGroups 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 GSE326978 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 GSE326978_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 PRJNA1344834 and SRA study SRP636628. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42155443) ↗
Study design
4 × RfxCas13d expressing HAP1 cells, bcgRNA-derived cDNA 10x vs 4 × RfxCas13d expressing HAP1 cells, mRNA-derived cDNA 10x vs 4 × RfxCas13d expressing MDA-MB-231 cells, bcgRNA-derived cDNA 10x vs 4 × RfxCas13d expressing MDA-MB-231 cells, mRNA-derived cDNA 10x

Supports a between-group comparison across 16 samples.

How we read this: 4 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.

Samples in this study
Datasets on a similar topic

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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.