Oxidation of thymine by TET2 dioxygenase carrying leukemia-derived neomorphic mutations
RNA-seq (gene expression) · mouse · 12 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
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × A vs 3 × B vs 3 × CGroups 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
- Neomorphic leukemia-derived mutations in the TET2 enzyme induce genome instability via a substrate shift from 5-methylcytosine to thymineProceedings of the National Academy of Sciences of the United States of America · 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 GSE278366_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 PRJNA1166881 and SRA study SRP535578. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 12 sample titles; they account for 9 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.
- GSM8545390 A-41 A
- GSM8545391 A-49 A
- GSM8545392 A-81 A
- GSM8545393 A-TET1KO
- GSM8545394 B-41 B
- GSM8545395 B-49 B
- GSM8545396 B-81 B
- GSM8545397 B-TET1KO
- GSM8545398 C-41 C
- GSM8545399 C-49 C
- GSM8545400 C-81 C
- GSM8545401 C-TET1KO
- GSE279386 Tp53 and Tet2 mutations cooperatively transform progenitors (RNA-Seq) 24 samples shares tet2, mutations
- GSE233516 DNA dioxygenase Tet2 regulates liver regeneration after partial hepatectomy. 18 samples shares tet2, dioxygenase
- GSE241310 TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-nascentRNA] 18 samples shares tet2, oxidation
- GSE243492 MALAT1 is required for phenotypic consequences of TET2 mutations in myeloid neoplasms. 12 samples shares tet2, mutations
- GSE285355 Tp53 and Tet2 mutations cooperatively transform GMP (RNA-Seq) 12 samples shares tet2, mutations
- GSE281880 Pathogen-derived glyoxylate inhibits Tet2 DNA dioxygenase to facilitate bacterial persister formation [II] 12 samples shares tet2, dioxygenase
- GSE281278 Pathogen-derived glyoxylate inhibits Tet2 DNA dioxygenase to facilitate bacterial persister formation 12 samples shares tet2, dioxygenase
- GSE233515 DNA dioxygenase Tet2 regulates liver regeneration after partial hepatectomy [dateset2] 9 samples shares tet2, dioxygenase
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.