Chromatin-associated LTR RNA m5C oxidation by TET2 regulates chromatin state and leukemogenesis [seq_DNA-ATAC_set2]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 54 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
- 54 samples: 10 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
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 GSE269958_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 peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1124379 and SRA study SRP514150. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 27 samples.
How we read this: 10 replicated groups read from 54 sample titles; they account for 27 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.
- GSM8331399 mESC, WT, ATAC, r1, set1 mESC, WT, ATAC, r1,
- GSM8331400 mESC, WT, ATAC, r2, set1 mESC, WT, ATAC, r2,
- GSM8331401 mESC, WT, ATAC, r3, set1 mESC, WT, ATAC, r3,
- GSM8331402 mESC, Tet2 KO, ATAC, r1, set1
- GSM8331403 mESC, Tet2 KO, ATAC, r2, set1
- GSM8331404 mESC, Tet2 KO, ATAC, r3, set1
- GSM8331405 mESC, WT; siNC, ATAC, r1, set1
- GSM8331406 mESC, WT; siNC, ATAC, r2, set1
- GSM8331407 mESC, WT; siNC, ATAC, r3, set1
- GSM8331408 mESC, Tet2 KO; siNC, ATAC, r1, set1
- GSM8331409 mESC, Tet2 KO; siNC, ATAC, r2, set1
- GSM8331410 mESC, Tet2 KO; siNC, ATAC, r3, set1
- GSM8331411 mESC, Tet2 KO; siMbd6, ATAC, r1, set1
- GSM8331412 mESC, Tet2 KO; siMbd6, ATAC, r2, set1
- GSM8331413 mESC, Tet2 KO; siMbd6, ATAC, r3, set1
- GSM8331414 mESC, Tet2 KO; siNsun2, ATAC, r1, set1
- GSM8331415 mESC, Tet2 KO; siNsun2, ATAC, r2, set1
- GSM8331416 mESC, Tet2 KO; siNsun2, ATAC, r3, set1
- GSM8331417 mESC, WT, ATAC, r1, set2 mESC, WT, ATAC, r1,
- GSM8331418 mESC, WT, ATAC, r2, set2 mESC, WT, ATAC, r2,
- GSM8331419 mESC, WT, ATAC, r3, set2 mESC, WT, ATAC, r3,
- GSM8331420 mESC, Pspc1 KO, ATAC, r1, set2
- GSM8331421 mESC, Pspc1 KO, ATAC, r2, set2
- GSM8331422 mESC, Pspc1 KO, ATAC, r3, set2
- GSM8331423 mESC, Tet2 KO; EV OE, ATAC, r1, set2
- GSM8331424 mESC, Tet2 KO; EV OE, ATAC, r2, set2
- GSM8331425 mESC, Tet2 KO; EV OE, ATAC, r3, set2
- GSM8331426 mESC, Tet2 KO; WT OE, ATAC, r1, set2
- GSM8331427 mESC, Tet2 KO; WT OE, ATAC, r2, set2
- GSM8331428 mESC, Tet2 KO; WT OE, ATAC, r3, set2
- GSM8331429 mESC, Tet2 KO; HxD OE, ATAC, r1, set2
- GSM8331430 mESC, Tet2 KO; HxD OE, ATAC, r2, set2
- GSM8331431 mESC, Tet2 KO; HxD OE, ATAC, r3, set2
- GSM8331432 mHSPC, WT; shNC, ATAC, r1 mHSPC, WT; shNC, ATAC,
- GSM8331433 mHSPC, WT; shNC, ATAC, r2 mHSPC, WT; shNC, ATAC,
- GSM8331434 mHSPC, WT; shNC, ATAC, r3 mHSPC, WT; shNC, ATAC,
- GSM8331435 mHSPC, Tet2 KO; shNC, ATAC, r1 mHSPC, Tet2 KO; shNC, A…
- GSM8331436 mHSPC, Tet2 KO; shNC, ATAC, r2 mHSPC, Tet2 KO; shNC, A…
- GSM8331437 mHSPC, Tet2 KO; shNC, ATAC, r3 mHSPC, Tet2 KO; shNC, A…
- GSM8331438 mHSPC, Tet2 KO; shMbd6, ATAC, r1 mHSPC, Tet2 KO; shMbd6,…
+ 14 more — browse all 54 samples with per-sample file links →
- 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, chromatin
- GSE241347 Chromatin-associated LTR RNA m5C oxidation by TET2 regulates leukemogenesis 291 samples shares tet2, ltr, chromatin-associated, leukemogenesis, oxidation, chromatin
- GSE241304 TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_DNA-CUTandTag] 24 samples shares tet2, ltr, leukemogenesis, oxidation
- GSE241342 TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-caRNA] 29 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
- GSE253164 Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_ATAC_with_blocking] 1 samples shares ltr, chromatin
- GSE253162 Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_ATAC_without_blocking] 1 samples shares ltr, chromatin
- GSE253165 Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease. 4 samples shares ltr, chromatin
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.