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Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cells

GSE308909 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2025/09/24 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 36 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
36 samples: 12 conditions, mostly in triplicateGroups 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
Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cellsCommunications biology · 2026
Summary (written by the submitters)
We have found that LbuCas13a exhibits collateral RNA cleavage activity in human cells after activation by the target RNA. Here we use total RNA sequencing to explore which RNAs are depleted by the collateral activity of LbuCas13a. ERCC spike-in RNAs were used for normalization between samples. This revealed near global depletion of mRNAs at 50 and 200 minutes after Cas13 protein and guide delivery. Mitochondrial and nuclear transcripts were not affected.
Published in
Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cells
Bot JF, Zhao Z, Li M et al. · Communications biology 2026 · PMID 41554880 · doi:10.1038/s42003-026-09511-3
This dataset
Open GSE308909 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 GSE308909_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 PRJNA1333378 and SRA study SRP625490. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41554880) ↗
Study design
12 conditions, mostly in triplicate
HAP1, Untreated, 50min, ×3 HAP1, Empty iTOP, 50min, ×3 HAP1, Non-targeting iTOP, 50min, ×3 HAP1, Targeting iTOP, 50min, ×3 HAP1, Untreated, 200min, ×3 HAP1, Empty iTOP, 200min, ×3 HAP1, Non-targeting iTOP, 200min, ×3 HAP1, Targeting iTOP, 200min, ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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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