Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [RNA-seq]
RNA-seq (gene expression) · mouse · 105 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
- Mus musculus (mouse)
- Samples
- 105 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 GSE208388_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 PRJNA859788 and SRA study SRP386910. 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.
+ 105 more — browse all 105 samples with per-sample file links →
- GSE252758 OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide (RNA-Seq) 4 samples shares transposable, elements, rna-seq
- GSE263284 BMAL1 represses transposable elements independently of CLOCK in pluripotent cells [ssRNA-seq] 4 samples shares transposable, elements, rna-seq
- GSE296548 Transposable elements are dynamically expressed within medium spiny neurons and associated with molecular and behavioral adaptations to cocaine [scRNA-seq] 3 samples shares transposable, elements, rna-seq
- GSE294558 Derepression of transposable elements in mouse prefrontal cortex disrupts social behavior 74 samples shares transposable, elements
- GSE288110 TBP regulates transposable element expression in early mouse embryos [RNA-seq] 49 samples shares transposable, rna-seq
- GSE276607 The retrotransposable element-silencing factor Daxx controls microglia identity and function in the adult brain [RNA-seq] 30 samples shares transposable, rna-seq
- GSE293906 Intestinal mast cell-derived leukotrienes mediate the anaphylactic response to ingested antigens 26 samples shares antigens, derived
- GSE297796 Cartography and mechanism of enhanced transcriptome plasticity by transposable elements 24 samples shares transposable, elements
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.