Epigenetic control over IFN Type-I response antagonizes self-renewal in acute myeloid leukemia
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 23 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)
- Topic
- Acute myeloid leukemiaThis series is part of our curated briefing on it.
- Samples
- 23 samples: 5 conditions, mostly with about 4 replicates eachGroups 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 GSE211643_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 PRJNA871242 and SRA study SRP393045. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 5 replicated groups read from 23 sample titles; they account for 16 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.
- GSM6481882 AA PHF8WT replicate 1 AA PHF8WT
- GSM6481883 AA PHF8WT replicate 2 AA PHF8WT
- GSM6481884 AA PHF8WT IgG
- GSM6481885 DD PHF8WT replicate 1 DD PHF8WT
- GSM6481886 DD PHF8WT replicate 2 DD PHF8WT
- 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,
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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.