TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-caRNA-m5C-MeRIP]
DNA methylation · human · 12 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Samples
- 12 samples: 3 × mESC, WT, caRNA, Input, vs 3 × mESC, WT, caRNA, m5C-IP, vs 3 × K562, WT, caRNA, Input, vs 3 × K562, WT, caRNA, m5C-IP,Groups 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
- RNA m(5)C oxidation by TET2 regulates chromatin state and leukaemogenesisNature · 2024
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 GSE241308_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: Look for beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA1007666 and SRA study SRP456148. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7720907 mESC, WT, caRNA, Input, rep1 mESC, WT, caRNA, Input,
- GSM7720908 mESC, WT, caRNA, Input, rep2 mESC, WT, caRNA, Input,
- GSM7720909 mESC, WT, caRNA, Input, rep3 mESC, WT, caRNA, Input,
- GSM7720910 mESC, WT, caRNA, m5C-IP, rep1 mESC, WT, caRNA, m5C-IP,
- GSM7720911 mESC, WT, caRNA, m5C-IP, rep2 mESC, WT, caRNA, m5C-IP,
- GSM7720912 mESC, WT, caRNA, m5C-IP, rep3 mESC, WT, caRNA, m5C-IP,
- GSM7720913 K562, WT, caRNA, Input, rep1 K562, WT, caRNA, Input,
- GSM7720914 K562, WT, caRNA, Input, rep2 K562, WT, caRNA, Input,
- GSM7720915 K562, WT, caRNA, Input, rep3 K562, WT, caRNA, Input,
- GSM7720916 K562, WT, caRNA, m5C-IP, rep1 K562, WT, caRNA, m5C-IP,
- GSM7720917 K562, WT, caRNA, m5C-IP, rep2 K562, WT, caRNA, m5C-IP,
- GSM7720918 K562, WT, caRNA, m5C-IP, rep3 K562, WT, caRNA, m5C-IP,
- GSE241342 TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-caRNA] 29 samples shares h2ak119ub, tet2, ltr, leukemogenesis, oxidation, histone
- GSE241304 TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_DNA-CUTandTag] 24 samples shares h2ak119ub, tet2, ltr, leukemogenesis, oxidation, histone
- GSE241347 Chromatin-associated LTR RNA m5C oxidation by TET2 regulates leukemogenesis 291 samples shares tet2, ltr, leukemogenesis, oxidation
- GSE269958 Chromatin-associated LTR RNA m5C oxidation by TET2 regulates chromatin state and leukemogenesis [seq_DNA-ATAC_set2] 54 samples shares tet2, ltr, leukemogenesis, oxidation
- GSE269959 Chromatin-associated LTR RNA m5C oxidation by TET2 regulates chromatin state and leukemogenesis [seq_DNA-CUTandTag] 41 samples shares tet2, ltr, leukemogenesis, oxidation
- GSE283531 MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia [RNA-Seq] 54 samples shares ltr, histone
- GSE283096 The histone acetyltransferase MOZ is a molecular dependency and therapeutic target in NUP98-rearranged acute myeloid leukemia [WGS, ATACseq, CUT&RUN, scRNAseq] 38 samples shares ltr, histone
- GSE261093 The TET2 methylcytosine dioxygenase regulates early and late transitions in exhausted CD8+ T-cell differentiation 51 samples shares tet2
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.