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PHF6 suppresses self-renewal of leukemic stem cells in AML

GSE270756 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 30 samples Submitted 2024/06/25 Platform GPL19057Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 30 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
30 samples: 8 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
PHF6 suppresses self-renewal of leukemic stem cells in AMLLeukemia · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
PHF6 suppresses self-renewal of leukemic stem cells in AML
Jalnapurkar SS, Pawar AS, George SS et al. · Leukemia 2024 · PMID 39004675 · doi:10.1038/s41375-024-02340-5
This dataset
Open GSE270756 in finder → Find more RNA-seq 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 GSE270756_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 PRJNA1128120 and SRA study SRP532593. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39004675) ↗
Study design
8 conditions, mostly with about 4 replicates each
CTRL_THP1_RNA-Seq ×5 Phf6 cKO LIC-e cells RNA-Seq ×4 Phf6 cKO Committed cells RNA-Seq ×4 Phf6 cKO LIC-e cells ATAC-Seq ×4 PHF6_KO_THP1_RNA-Seq ×4 Ctrl LIC-e cells RNA-Seq ×3 Ctrl Committed cells RNA-Seq ×3 Ctrl LIC-e cells ATAC-Seq ×3

Supports a between-group comparison across 30 samples.

How we read this: 8 replicated groups read from 30 sample titles; they account for 30 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
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