Transcriptomic changes in THP1 human AML cell line on PHF6 knockout, PHF6R274Q mutation, PHIP knockout, and double knockout of PHF6 and PHIP compared to wildtype cells
RNA-seq (gene expression) · human · 21 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
- 21 samples: 5 conditions, mostly with about 5 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
- Leukemia mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemnessGenes & development · 2025
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 GSE281475_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 PRJNA1183968 and SRA study SRP544130. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 5 replicated groups read from 21 sample titles; they account for 21 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.
- GSM8621563 WT_THP1_RNA-Seq_Rep1 WT_THP1_RNA-Seq
- GSM8621564 WT_THP1_RNA-Seq_Rep2 WT_THP1_RNA-Seq
- GSM8621565 WT_THP1_RNA-Seq_Rep3 WT_THP1_RNA-Seq
- GSM8621566 WT_THP1_RNA-Seq_Rep4 WT_THP1_RNA-Seq
- GSM8621567 WT_THP1_RNA-Seq_Rep5 WT_THP1_RNA-Seq
- GSM8621568 PHF6KO_THP1_RNA-Seq_Rep1 PHF6KO_THP1_RNA-Seq
- GSM8621569 PHF6KO_THP1_RNA-Seq_Rep2 PHF6KO_THP1_RNA-Seq
- GSM8621570 PHF6KO_THP1_RNA-Seq_Rep3 PHF6KO_THP1_RNA-Seq
- GSM8621571 PHF6KO_THP1_RNA-Seq_Rep4 PHF6KO_THP1_RNA-Seq
- GSM8621572 PHF6KO_THP1_RNA-Seq_Rep5 PHF6KO_THP1_RNA-Seq
- GSM8621573 R274Q_THP1_RNA-Seq_Rep1 R274Q_THP1_RNA-Seq
- GSM8621574 R274Q_THP1_RNA-Seq_Rep2 R274Q_THP1_RNA-Seq
- GSM8621575 R274Q_THP1_RNA-Seq_Rep3 R274Q_THP1_RNA-Seq
- GSM8621576 R274Q_THP1_RNA-Seq_Rep4 R274Q_THP1_RNA-Seq
- GSM8621577 R274Q_THP1_RNA-Seq_Rep5 R274Q_THP1_RNA-Seq
- GSM8621578 PHIPKO_THP1_RNA-Seq_Rep1 PHIPKO_THP1_RNA-Seq
- GSM8621579 PHIPKO_THP1_RNA-Seq_Rep2 PHIPKO_THP1_RNA-Seq
- GSM8621580 PHIPKO_THP1_RNA-Seq_Rep3 PHIPKO_THP1_RNA-Seq
- GSM8621581 DKO_THP1_RNA-Seq_Rep1 DKO_THP1_RNA-Seq
- GSM8621582 DKO_THP1_RNA-Seq_Rep2 DKO_THP1_RNA-Seq
- GSM8621583 DKO_THP1_RNA-Seq_Rep3 DKO_THP1_RNA-Seq
- GSE281627 Changes in H3K27 acetylation in THP1 human AML cell line on PHF6 knockout, PHF6R274Q mutation, PHIP knockout, and double knockout of PHF6 and PHIP compared to wildtype clones 18 samples shares phf6r274q, thp1, phf6, phip, aml, knockout, mutation, compared
- GSE281624 Transcriptomic changes in PHF6 knockout THP1 human AML cell line on rescue with PHF6 wildtype (with and without PHIP) or rescue with PHF6R274Q mutant 19 samples shares phf6r274q, thp1, phf6, phip, aml, knockout
- GSE281628 PHF6 occupancy in THP1 human AML cell line in wildtype, PHF6R274Q mutant, and PHIP knockout cells 12 samples shares phf6r274q, thp1, phf6, phip, aml, knockout
- GSE277149 Transcriptome changes caused by PHF6 knockout in THP1 human AML cell line 9 samples shares thp1, phf6, aml, knockout
- GSE281626 Chromatin accessibility changes caused by PHF6 knockout in THP1 human AML cell line 9 samples shares thp1, phf6, aml, knockout
- GSE281629 PHIP occupancy in THP1 human AML cell line 4 samples shares thp1, phip, aml
- GSE288498 The Retinal Determination Gene Network can confer chemoresistant properties to AML [THP1_chip_rna] 23 samples shares thp1, aml
- GSE239783 mRNA-seq of wild-type or ZUFSP knockout THP1 cells after vesicular stomatitis virus infection 4 samples shares thp1, knockout
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.