hMeDIP sequencing of human leukemia cells
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: 12 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE99953_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 PRJNA390176 and SRA study SRP109034. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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.
- GSM2666417 HL60-0-hrs-1-hMeDIP
- GSM2666418 HL60-0-hrs-1-input
- GSM2666419 HL60-0-hrs-2-hMeDIP
- GSM2666420 HL60-0-hrs-2-input
- GSM2666421 HL60-0-hrs-3-hMeDIP
- GSM2666422 HL60-0-hrs-3-input
- GSM2666423 HL60-72-hrs-1-hMeDIP
- GSM2666424 HL60-72-hrs-1-input
- GSM2666425 HL60-72-hrs-2-hMeDIP
- GSM2666426 HL60-72-hrs-2-input
- GSM2666427 HL60-72-hrs-3-hMeDIP
- GSM2666428 HL60-72-hrs-3-input
- GSE256354 Hypomethylating agents induce epigenetic and transcriptional heterogeneity with implications for acute myeloid leukemia cell self-renewal 2765 samples shares leukemia
- GSE234558 Tracking rare single donor and recipient immune and leukemia cells after allogeneic hematopoietic cell transplantation using mitochondrial DNA mutations 85 samples shares leukemia
- GSE268035 STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia 541 samples shares leukemia
- GSE240497 Activation of a nongenetic AHR-ELMSAN1 axis optimizes BET-targeting therapy and suppresses leukemia stem cells in preclinical models 66 samples shares leukemia
- GSE294601 CD371-Targeted CAR T-cells Secreting Interleukin-18 Exhibit Robust Expansion and Clearance of Refractory Acute Myeloid Leukemia 52 samples shares leukemia
- GSE18700 Genome-wide DNA methylation profiling of Acute Myeloid Leukemia 352 samples shares leukemia
- GSE190785 Dual Targeting of FLT3 and LSD1 Disrupts the MYC Super Enhancer Complex in Acute Myeloid Leukemia. 289 samples shares leukemia
- GSE270185 Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemia 249 samples shares leukemia
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.