Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing
RNA-seq (gene expression) · human · 20 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
- 20 samples: 8 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
- Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencingeLife · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE254194_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1068978 and SRA study SRP485897. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 8 replicated groups read from 20 sample titles; they account for 20 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.
- GSM8035712 HEK293T, DRAM-ABE, replicate 1 HEK293T, DRAM-ABE,
- GSM8035713 HEK293T, DRAM-ABE, replicate 2 HEK293T, DRAM-ABE,
- GSM8035714 HEK293T, DRAM-ABE, replicate 3 HEK293T, DRAM-ABE,
- GSM8035715 HEK293T, NSUN2KO-DRAM-ABE, replicate 1 HEK293T, NSUN2KO-DRAM-A…
- GSM8035716 HEK293T, NSUN2KO-DRAM-ABE, replicate 2 HEK293T, NSUN2KO-DRAM-A…
- GSM8035717 HEK293T, NSUN2KO-DRAM-ABE, replicate 3 HEK293T, NSUN2KO-DRAM-A…
- GSM8035718 HEK293T, NSUN6KO-DRAM-ABE, replicate 1 HEK293T, NSUN6KO-DRAM-A…
- GSM8035719 HEK293T, NSUN6KO-DRAM-ABE, replicate 2 HEK293T, NSUN6KO-DRAM-A…
- GSM8035720 HEK293T, DRAM-CBE, replicate 1 HEK293T, DRAM-CBE,
- GSM8035721 HEK293T, DRAM-CBE, replicate 2 HEK293T, DRAM-CBE,
- GSM8035722 HEK293T, DRAM-CBE, replicate 3 HEK293T, DRAM-CBE,
- GSM8035723 HEK293T, NSUN2KO-DRAM-CBE, replicate 1 HEK293T, NSUN2KO-DRAM-C…
- GSM8035724 HEK293T, NSUN2KO-DRAM-CBE, replicate 2 HEK293T, NSUN2KO-DRAM-C…
- GSM8035725 HEK293T, NSUN2KO-DRAM-CBE, replicate 3 HEK293T, NSUN2KO-DRAM-C…
- GSM8035726 HEK293T, NSUN6KO-DRAM-CBE, replicate 1 HEK293T, NSUN6KO-DRAM-C…
- GSM8035727 HEK293T, NSUN6KO-DRAM-CBE, replicate 2 HEK293T, NSUN6KO-DRAM-C…
- GSM8035728 HEK293T, TadA, replicate 1 HEK293T, TadA,
- GSM8035729 HEK293T, TadA, replicate 2 HEK293T, TadA,
- GSM8035730 HEK293T, APOBEC1, replicate 1 HEK293T, APOBEC1,
- GSM8035731 HEK293T, APOBEC1, replicate 2 HEK293T, APOBEC1,
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- GSE248461 An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP II] 14 samples shares transcriptome-wide
- GSE301521 FOCAS: Transcriptome-wide screening of individual m6A sites functionally dissects epitranscriptomic control of gene expression in cancer [FOCAS_4cellline_RNAseq] 72 samples shares transcriptome-wide
- GSE293987 A Workflow for Transcriptome-wide Assessment of Antisense Oligonucleotide Selectivity 53 samples shares transcriptome-wide
- GSE244424 Identification of potential targets of PPDPF in cholangiacarcinoma via transcriptome-wide RNA-seq 6 samples shares transcriptome-wide
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.