Epigenetic Control over IFN Type-I Response antagonizes self-renewal in acute myeloid leukemia (RNA-seq)
RNA-seq (gene expression) · human · 18 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
- Homo sapiens (human)
- Samples
- 18 samples: 4 × THP1 F279S, vs 4 × THP1 PHF8, vs 4 × THP1 wt,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
- Epigenetic control over the cell-intrinsic immune response antagonizes self-renewal in acute myeloid leukemiaBlood · 2024
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 GSE211642_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 PRJNA871248 and SRA study SRP393045. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 3 replicated groups read from 18 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.
- GSM6481887 THP1+ERAA, rep1, d3
- GSM6481888 THP1+ERAA, rep2, d3
- GSM6481889 THP1+ERDD, rep1, d3
- GSM6481890 THP1+ERDD, rep2, d3
- GSM6481891 THP1+ERPHF8, rep1, d3
- GSM6481892 THP1+ERPHF8, rep2, d3
- GSM6481893 THP1 F279S, rep1 THP1 F279S,
- GSM6481894 THP1 F279S, rep2 THP1 F279S,
- GSM6481895 THP1 F279S, rep3 THP1 F279S,
- GSM6481896 THP1 F279S, rep4 THP1 F279S,
- GSM6481897 THP1 PHF8, rep1 THP1 PHF8,
- GSM6481898 THP1 PHF8, rep2 THP1 PHF8,
- GSM6481899 THP1 PHF8, rep3 THP1 PHF8,
- GSM6481900 THP1 PHF8, rep4 THP1 PHF8,
- GSM6481901 THP1 wt, rep1 THP1 wt,
- GSM6481902 THP1 wt, rep2 THP1 wt,
- GSM6481903 THP1 wt, rep3 THP1 wt,
- GSM6481904 THP1 wt, rep4 THP1 wt,
- GSE256354 Hypomethylating agents induce epigenetic and transcriptional heterogeneity with implications for acute myeloid leukemia cell self-renewal 2765 samples shares self-renewal, epigenetic, leukemia, myeloid
- GSE290771 Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B [RNA-seq_2] 12 samples shares epigenetic, control, rna-seq
- GSE256495 Convergent Epigenetic Evolution Drives Relapse in Acute Myeloid Leukemia 195 samples shares epigenetic, leukemia, myeloid
- GSE249080 Epigenetic Regulation of Non-canonical Menin Targets Modulates Menin Inhibitor Response in Acute Myeloid Leukemia 40 samples shares epigenetic, leukemia, myeloid
- GSE290418 Bulk RNA-sequencing of human non-IBD enteroids treated with interferon-gamma (IFNγ) 12 samples shares ifn, rna-seq
- GSE294916 IFNγ-induced memory in human macrophages is not sustained by epigenetic changes but the durability of the cytokine itself [CUT&Tag] 28 samples shares ifn, epigenetic
- GSE234181 Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq] 184 samples shares epigenetic, rna-seq
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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.