H4K20me3 erasure facilitates reprogramming to totipotent-like state by promoting DUX4 mediated transcription [RNA-Seq]
RNA-seq (gene expression) · human · 12 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
- 12 samples: 6 conditions, mostly in duplicateGroups 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.
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 GSE287564_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 PRJNA1213755 and SRA study SRP558713. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 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.
- GSM8748048 DMSO_rep1 DMSO
- GSM8748049 DMSO_rep2 DMSO
- GSM8748050 A196_rep1 A196
- GSM8748051 A196_rep2 A196
- GSM8748052 DUX4OE_rep1 DUX4OE
- GSM8748053 DUX4OE_rep2 DUX4OE
- GSM8748054 A196DUX4OE_rep1 A196DUX4OE
- GSM8748055 A196DUX4OE_rep2 A196DUX4OE
- GSM8748056 PlaB_rep1 PlaB
- GSM8748057 PlaB_rep2 PlaB
- GSM8748058 A196PlaB_rep1 A196PlaB
- GSM8748059 A196PlaB_rep2 A196PlaB
- GSE342322 APE1-Mediated Transcriptional Reprogramming in Esophageal Adenocarcinoma Cells under Acidic Bile Reflux Stress 36 samples shares reprogramming, transcription, mediated
- GSE266253 DNAJB1-PRKACA fusion drives fibrolamellar liver cancer through impaired SIK signaling and CRTC2/p300-mediated transcriptional reprogramming 12 samples shares reprogramming, transcription, mediated
- GSE299603 DUX4 activates a transcriptional network involving Krüppel-like factors KLF17 and KLF18 [KLF17_KLF18_OE] 9 samples shares dux4, transcription
- GSE272002 LSD1 inhibitor, TAS1440, disrupts INSM1-LSD1 complex activating tumor-suppressive pathways via transcriptional reprogramming in neuroendocrine SCLC 324 samples shares reprogramming, transcription
- GSE249544 Phenotypical states modulate sensitivity and transcriptional reprogramming in patient-derived glioblastoma cells in response to temozolomide and radiation therapy. [RNA-Seq] 48 samples shares reprogramming, transcription
- GSE298471 A combinatorial transcription factor screening platform for immune cell reprogramming [scRNA-seq] 46 samples shares reprogramming, transcription
- GSE267498 Generation of hiPSC-derived brain microvascular endothelial cells using a combination of directed differentiation and transcriptional reprogramming strategies 37 samples shares reprogramming, transcription
- GSE261322 NF-κB- and TET2-mediated macrophage reprogramming overrides the anti-inflammatory effects of hypoxia and improves responses in human cancer (RNA-Seq I). 20 samples shares reprogramming, mediated
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.