GEO series
Human ribomes reveal DNA-embedded ribonucleotides as epigenetic modulators of DNA supercoiling
GSE297046
Homo sapiens (human)
DNA methylation
40 samples
Submitted 2026/07/14
Platform GPL20795Platform GPL21697Platform GPL16791Platform GPL34284
At a glance
DNA methylation · human · 40 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Samples
- 40 samples: 9 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)
The goal of this study is to analyze distribution and enrichment of ribonucleotide embedment in human genome in various genomic regions of funcitonal relevance and association with gene expression and methylation levels.
This dataset
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.
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 GSE297046_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA1257959 and SRA study SRP583138. Searching any of these in the dataset finder brings you back here.
Study design
9 conditions, mostly in duplicate
Whole genome bisulfite-seq of CD4T ×4
ribose-seq of CD4T genomic DNA with dsF+RE1 f… ×3
ribose-seq of hESC-H9 genomic DNA with dsF fr… ×2
ribose-seq of HEK293T genomic DNA with dsF fr… ×2
ribose-seq of HEK293T RNase H2 KO (T3-8) geno… ×2
ribose-seq of HEK293T RNase H2 KO (T3-17) gen… ×2
RNA-seq of HEK293T-RNH2AKO-T3-17 ×2
RNA-seq of HEK293T-RNH2AKO-T3-8 ×2
+20 more
Supports a between-group comparison across 21 samples.
How we read this: 9 replicated groups read from 40 sample titles; they account for 21 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
- GSM8982461 Whole genome bisulfite-seq of CD4T-1 Whole genome bisulfite-…
- GSM8982462 Whole genome bisulfite-seq of CD4T-2 Whole genome bisulfite-…
- GSM8982464 Whole genome bisulfite-seq of CD4T-3 Whole genome bisulfite-…
- GSM8982465 Whole genome bisulfite-seq of CD4T-4 Whole genome bisulfite-…
- GSM8982467 Whole genome DNA-seq of CD4T-1 with dsF fragmentation
- GSM8982468 Whole genome DNA-seq of CD4T-1 with RE1 fragmentation
- GSM8982469 Whole genome DNA-seq of CD4T-1 with RE2 fragmentation
- GSM8982470 Whole genome DNA-seq of CD4T-1 with RE3 fragmentation
- GSM8982472 ribose-seq of CD4T genomic DNA with dsF fragmentation
- GSM8982473 ribose-seq of CD4T genomic DNA with RE1 fragmentation
- GSM8982474 ribose-seq of CD4T genomic DNA with dsF+RE1 fragmentation, replicate 1 ribose-seq of CD4T geno…
- GSM8982476 ribose-seq of CD4T genomic DNA with dsF+RE1 fragmentation, replicate 2 ribose-seq of CD4T geno…
- GSM8982477 ribose-seq of CD4T genomic DNA with dsF+RE1 fragmentation, replicate 3 ribose-seq of CD4T geno…
- GSM8982478 ribose-seq of hESC-H9 genomic DNA with dsF fragmentation, replicate 1 ribose-seq of hESC-H9 g…
- GSM8982479 ribose-seq of hESC-H9 genomic DNA with dsF fragmentation, replicate 2 ribose-seq of hESC-H9 g…
- GSM8982480 ribose-seq of hESC-H9 genomic DNA with RE1 fragmentation
- GSM8982482 ribose-seq of hESC-H9 genomic DNA with dsF+RE1 fragmentation
- GSM8982483 ribose-seq of HEK293T genomic DNA with RE1 fragmentation
- GSM8982484 ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with RE1 fragmentation
- GSM8982485 ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with RE1 fragmentation
- GSM8982487 ribose-seq of hESC-H9 genomic DNA with RE3 fragmentation
- GSM8982488 ribose-seq of HEK293T genomic DNA with RE3 fragmentation
- GSM8982489 ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with RE2 fragmentation
- GSM8982490 ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with RE2 fragmentation
- GSM8982492 ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with RE3 fragmentation
- GSM8982493 ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with RE3 fragmentation
- GSM8982494 ribose-seq of HEK293T genomic DNA with dsF fragmentation, replicate 1 ribose-seq of HEK293T g…
- GSM8982495 ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with dsF fragmentation, replicate 1 ribose-seq of HEK293T R…
- GSM8982496 ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with dsF fragmentation, replicate 1 ribose-seq of HEK293T R…
- GSM8982497 ribose-seq of hESC-H9 genomic DNA with RE2 fragmentation
- GSM8982499 ribose-seq of HEK293T genomic DNA with RE2 fragmentation
- GSM8982500 ribose-seq of HEK293T genomic DNA with dsF fragmentation, replicate 2 ribose-seq of HEK293T g…
- GSM8982501 ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with dsF fragmentation, replicate 2 ribose-seq of HEK293T R…
- GSM8982502 ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with dsF fragmentation, replicate 2 ribose-seq of HEK293T R…
- GSM8982503 RNA-seq of HEK293T-RNH2AKO-T3-17 replicate 1 RNA-seq of HEK293T-RNH2…
- GSM8982505 RNA-seq of HEK293T-RNH2AKO-T3-17 replicate 2 RNA-seq of HEK293T-RNH2…
- GSM8982506 RNA-seq of HEK293T-RNH2AKO-T3-8 replicate 1 RNA-seq of HEK293T-RNH2…
- GSM8982507 RNA-seq of HEK293T-RNH2AKO-T3-8 replicate 2 RNA-seq of HEK293T-RNH2…
- GSM8982508 RNA-seq of HEK293-WT replicate 1 RNA-seq of HEK293-WT
- GSM8982509 RNA-seq of HEK293-WT replicate 2 RNA-seq of HEK293-WT
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