GEO series

Chromatin-associated LTR RNA m5C oxidation by TET2 regulates leukemogenesis

GSE241347 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 291 samples Submitted 2024/07/24 Platform GPL24247Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 291 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 291 samples: 96 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: RNA m(5)C oxidation by TET2 regulates chromatin state and leukaemogenesisNature · 2024

SuperSeries — this record groups several sub-series.

Summary (written by the submitters)

This SuperSeries is composed of the SubSeries listed below.

Published in

RNA m(5)C oxidation by TET2 regulates chromatin state and leukaemogenesis

Zou Z, Dou X, Li Y et al. · Nature 2024 · PMID 39358506 · doi:10.1038/s41586-024-07969-x

This dataset

Open GSE241347 in finder → Find more ChIP / ATAC / CUT&Tag 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 GSE241347_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1007723 and SRA study SRP514150. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39358506) ↗

Study design

96 conditions, mostly in triplicate

mESC, Tet2 KO, H2AK119ub, CUT&Tag, ×5 mESC, WT, caRNA, Input, ×3 mESC, WT, caRNA, m5C-IP, ×3 K562, WT, caRNA, Input, ×3 K562, WT, caRNA, m5C-IP, ×3 mESC, Tet2 WT, nascentRNA, 10m, ×3 mESC, Tet2 WT, nascentRNA, 20m, ×3 mESC, Tet2 WT, nascentRNA, 40m, ×3 +118 more

Supports a between-group comparison across 261 samples.

How we read this: 96 replicated groups read from 291 sample titles; they account for 261 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

GSM7720788 mESC, Tet2 WT, ATAC, rep1 mESC, Tet2 WT, ATAC,
GSM7720789 mESC, Tet2 WT, ATAC, rep2 mESC, Tet2 WT, ATAC,
GSM7720790 mESC, Tet2 KO, ATAC, rep1 mESC, Tet2 KO, ATAC,
GSM7720791 mESC, Tet2 KO, ATAC, rep2 mESC, Tet2 KO, ATAC,
GSM7720792 mESC, Pspc1 WT, ATAC, rep1 mESC, Pspc1 WT, ATAC,
GSM7720793 mESC, Pspc1 WT, ATAC, rep2 mESC, Pspc1 WT, ATAC,
GSM7720794 mESC, Pspc1 KO, ATAC, rep1 mESC, Pspc1 KO, ATAC,
GSM7720795 mESC, Pspc1 KO, ATAC, rep2 mESC, Pspc1 KO, ATAC,
GSM7720796 mLK, Tet2 WT, ATAC, rep1 mLK, Tet2 WT, ATAC,
GSM7720797 mLK, Tet2 WT, ATAC, rep2 mLK, Tet2 WT, ATAC,
GSM7720798 mLK, Tet2 KO, ATAC, rep1 mLK, Tet2 KO, ATAC,
GSM7720799 mLK, Tet2 KO, ATAC, rep2 mLK, Tet2 KO, ATAC,
GSM7720826 mESC, Tet2 WT, H2AK119ub, CUT&Tag, rep1 mESC, Tet2 WT, H2AK119u…
GSM7720827 mESC, Tet2 WT, H2AK119ub, CUT&Tag, rep2 mESC, Tet2 WT, H2AK119u…
GSM7720828 mESC, Tet2 KO, H2AK119ub, CUT&Tag, rep1 mESC, Tet2 KO, H2AK119u…
GSM7720829 mESC, Tet2 KO, H2AK119ub, CUT&Tag, rep2 mESC, Tet2 KO, H2AK119u…
GSM7720830 mESC, Tet2 WT, H3K27me3, CUT&Tag, rep1 mESC, Tet2 WT, H3K27me3…
GSM7720831 mESC, Tet2 WT, H3K27me3, CUT&Tag, rep2 mESC, Tet2 WT, H3K27me3…
GSM7720832 mESC, Tet2 KO, H3K27me3, CUT&Tag, rep1 mESC, Tet2 KO, H3K27me3…
GSM7720833 mESC, Tet2 KO, H3K27me3, CUT&Tag, rep2 mESC, Tet2 KO, H3K27me3…
GSM7720834 mLK, Tet2 WT, H2AK119ub, CUT&Tag, rep1 mLK, Tet2 WT, H2AK119ub…
GSM7720835 mLK, Tet2 WT, H2AK119ub, CUT&Tag, rep2 mLK, Tet2 WT, H2AK119ub…
GSM7720836 mLK, Tet2 KO, H2AK119ub, CUT&Tag, rep1 mLK, Tet2 KO, H2AK119ub…
GSM7720837 mLK, Tet2 KO, H2AK119ub, CUT&Tag, rep2 mLK, Tet2 KO, H2AK119ub…
GSM7720838 mLK, Tet2 WT, H3K27me3, CUT&Tag, rep1 mLK, Tet2 WT, H3K27me3,…
GSM7720839 mLK, Tet2 WT, H3K27me3, CUT&Tag, rep2 mLK, Tet2 WT, H3K27me3,…
GSM7720840 mLK, Tet2 KO, H3K27me3, CUT&Tag, rep1 mLK, Tet2 KO, H3K27me3,…
GSM7720841 mLK, Tet2 KO, H3K27me3, CUT&Tag, rep2 mLK, Tet2 KO, H3K27me3,…
GSM7720842 K562, siControl, H2AK119ub, CUT&Tag, rep1 K562, siControl, H2AK11…
GSM7720843 K562, siControl, H2AK119ub, CUT&Tag, rep2 K562, siControl, H2AK11…
GSM7720844 K562, siMBD6, H2AK119ub, CUT&Tag, rep1 K562, siMBD6, H2AK119ub…
GSM7720845 K562, siMBD6, H2AK119ub, CUT&Tag, rep2 K562, siMBD6, H2AK119ub…
GSM7720846 K562, TET2 WT, H2AK119ub, CUT&Tag, rep1 K562, TET2 WT, H2AK119u…
GSM7720847 K562, TET2 WT, H2AK119ub, CUT&Tag, rep2 K562, TET2 WT, H2AK119u…
GSM7720848 K562, TET2 KO, H2AK119ub, CUT&Tag, rep1 K562, TET2 KO, H2AK119u…
GSM7720849 K562, TET2 KO, H2AK119ub, CUT&Tag, rep2 K562, TET2 KO, H2AK119u…
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,

+ 251 more — browse all 291 samples with per-sample file links →

Datasets on a similar topic

GSE269958 Chromatin-associated LTR RNA m5C oxidation by TET2 regulates chromatin state and leukemogenesis [seq_DNA-ATAC_set2] 54 samples shares tet2, ltr, chromatin-associated, leukemogenesis, oxidation
GSE269959 Chromatin-associated LTR RNA m5C oxidation by TET2 regulates chromatin state and leukemogenesis [seq_DNA-CUTandTag] 41 samples shares tet2, ltr, chromatin-associated, leukemogenesis, oxidation
GSE241342 TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-caRNA] 29 samples shares tet2, ltr, leukemogenesis, oxidation
GSE241304 TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_DNA-CUTandTag] 24 samples shares tet2, ltr, leukemogenesis, oxidation
GSE241308 TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-caRNA-m5C-MeRIP] 12 samples shares tet2, ltr, leukemogenesis, oxidation
GSE261093 The TET2 methylcytosine dioxygenase regulates early and late transitions in exhausted CD8+ T-cell differentiation 51 samples shares tet2
GSE267609 Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate 63 samples shares ltr
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

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