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Programmable RNA acetylation with CRISPR-Cas13

GSE293920 Homo sapiens (human) RNA-seq (gene expression) 56 samples Submitted 2025/04/08 Platform GPL34281Platform GPL34328
At a glance

RNA-seq (gene expression) · human · 56 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
56 samples: 24 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)
Recent studies claim that N4-acetylcytidine (ac4C) modification of RNA confers crucial regulatory roles, such as increasing translation efficiency and prolonging its half-life. However, the absence of methods for selectively acetylating specific RNA molecules hampers linking ac4C to cell physiology. Here, we developed an efficient molecular tool that incorporates ac4C on a specific transcript of interest.
Read the full summary ↓
Through protein engineering, we developed a hyperactive variant of N-acetyltransferase 10 (NAT10), designated eNAT10. When fused to the programmable RNA-targeting protein dCas13, eNAT10 enables robust acetylation of various target RNAs in multiple contexts. RNA acetylation by dCas13-eNAT10 was highly dependent on co-transfected guide RNA, highlighting its specificity. We also describe the first programmable RNA chemical modification in vivo using dual-AAV. Utilizing our system, we found that acetylation of RNA may modulate the subcellular localization of modified transcripts. We anticipate that our tool will facilitate numerous studies on ac4C functions across different cellular and disease contexts.
This dataset
Open GSE293920 in finder → Find more 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 GSE293920_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 PRJNA1247425 and SRA study SRP577050. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
24 conditions, mostly in duplicate
HEK293T, dCas13-NES-eNAT10 and NT gRNA transf… ×3 HEK293T, dCas13-NES-eNAT10 and T gRNA transfe… ×3 HEK293T, dCas13-NES-edNAT10 and T gRNA transf… ×3 HEK293T, dCas13-NES-eNAT10 and NT gRNA transf… ×3 HEK293T, dCas13-NES-eNAT10 and T gRNA transfe… ×3 HEK293T, dCas13-NES-edNAT10 and T gRNA transf… ×3 HEK293T, dCas13-NES-eNAT10 transfection, ×3 HEK293T, dCas13-NES-edNAT10 transfection, ×3 +16 more

Supports a case/control comparison: 4 samples read as cases, 17 as controls.

How we read this: 24 replicated groups read from 56 sample titles; they account for 56 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

+ 16 more — browse all 56 samples with per-sample file links →

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.