DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts [RNA-Seq]
RNA-seq (gene expression) · human · 60 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
- 60 samples
- 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.
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 GSE209772_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 PRJNA862388 and SRA study SRP388192. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 60 more — browse all 60 samples with per-sample file links →
- GSE309034 Combined BET Bromodomain and DNMT Inhibition Targets Lineage Plasticity in Prostate Cancer [BETi_DNMTi_human_RNAseq] 44 samples shares dnmt, inhibition
- GSE305560 TP53-Agnostic Lethality through Combined Pan-HDAC and CDK Inhibition in Acute Myeloid Leukemia 18 samples shares hdac, inhibition
- GSE280100 RNA-sequencing analysis of differential expressed genes in TGFβ-treated HK-2 cells after HDAC11 inhibition 15 samples shares hdac, inhibition
- GSE316603 HDAC3 inhibition as a therapeutic strategy in T-cell acute lymphoblastic leukemia via the TYK2-STAT1-BCL2 signaling pathway 12 samples shares hdac, inhibition
- GSE309499 HDAC5 Deficiency Induces Intrinsic Resistance to KRASG12D Inhibition by Disrupting c-Myc Acetylation-Ubiquitination Homeostasis [RNA-seq] 12 samples shares hdac, inhibition
- GSE268034 GNAS knockout potentiates HDAC3 inhibition through viral mimicry-related interferon responses in lymphoma 12 samples shares hdac, inhibition
- GSE281320 DNMT3B promotes neuroblastoma growth and survival, and its inhibition demonstrates antitumor effects. 6 samples shares dnmt, inhibition
- GSE301514 ID3 Deficiency Alters Chromatin Accessibility at DSB Sites and Enhances Vulnerability to HDAC Inhibition [ATAC-seq] 12 samples shares hdac, inhibition
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.