GEO series

G-quadruplexes within the SVA retrotransposon modulate TAF1 gene expression in X-linked Dystonia Parkinsonism [RNA-Seq]

GSE250293 Homo sapiens (human) RNA-seq (gene expression) 63 samples Submitted 2024/09/04 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 63 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: 63 samples: 21 conditions, mostly in triplicateGroups 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: G-quadruplexes in an SVA retrotransposon cause aberrant TAF1 gene expression in X-linked dystonia parkinsonismNucleic acids research · 2024

Summary (written by the submitters)

X-linked dystonia parkinsonism (XDP) is an inherited neurodegenerative disease characterized by the antisense insertion of an SVA retrotransposon into the TAF1 gene, encoding for the largest subunit of the basal transcription factor TFIID, which is essential for RNA polymerase II activity. This SVA insertion has been associated with altered TAF1 expression levels, but the cause of this outcome and its link to the development of XDP remain unknown.

Read the full summary ↓

Unique to the XDP SVA compared to other SVA retrotransposons in the human genome is the amplification of the (GGGAGA)n repeat domain, creating a unique G4-prone region, whose length correlates with age at onset and disease severity. By ChIP-seq and ChIP-qPCR with the anti-G4 antibody BG4, we assessed that G4s are present in the folded state in the XDP SVA of these cells. Using available G4 ligands, we demonstrated that stabilization of the XDP SVA G4s reduces TAF1 transcripts in the exons around and downstream of the SVA, while increasing the transcription of the upstream exons, possibly through a positive feedback loop.

Published in

G-quadruplexes in an SVA retrotransposon cause aberrant TAF1 gene expression in X-linked dystonia parkinsonism

Nicoletto G, Terreri M, Maurizio I et al. · Nucleic acids research 2024 · PMID 39287133 · doi:10.1093/nar/gkae797

This dataset

Open GSE250293 in finder → Find more human 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 GSE250293_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: 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 PRJNA1053321 and SRA study SRP478259. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39287133) ↗

Study design

21 conditions, mostly in triplicate

Ctrl NPCs, NT, ×3 Ctrl NPCs, B19, ×3 Ctrl NPCs, Q, ×3 NMC hFib, NT, ×3 NMC hFib, B19, ×3 NMC hFib, Q, ×3 XDP hFib, NT, ×3 XDP hFib, B19, ×3 +13 more

Supports a between-group comparison across 63 samples.

How we read this: 21 replicated groups read from 63 sample titles; they account for 63 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

GSM7976985 Ctrl NPCs, NT, rep1 Ctrl NPCs, NT,
GSM7976986 Ctrl NPCs, NT, rep2 Ctrl NPCs, NT,
GSM7976987 Ctrl NPCs, B19, rep1 Ctrl NPCs, B19,
GSM7976988 Ctrl NPCs, B19, rep2 Ctrl NPCs, B19,
GSM7976989 Ctrl NPCs, Q, rep1 Ctrl NPCs, Q,
GSM7976990 Ctrl NPCs, Q, rep2 Ctrl NPCs, Q,
GSM7977000 NMC hFib, NT, rep1 NMC hFib, NT,
GSM7977001 NMC hFib, NT, rep2 NMC hFib, NT,
GSM7977002 NMC hFib, B19, rep1 NMC hFib, B19,
GSM7977003 NMC hFib, B19, rep2 NMC hFib, B19,
GSM7977004 NMC hFib, Q, rep1 NMC hFib, Q,
GSM7977005 NMC hFib, Q, rep2 NMC hFib, Q,
GSM7977006 XDP hFib, NT, rep1 XDP hFib, NT,
GSM7977007 XDP hFib, NT, rep2 XDP hFib, NT,
GSM7977008 XDP hFib, B19, rep1 XDP hFib, B19,
GSM7977009 XDP hFib, B19, rep2 XDP hFib, B19,
GSM7977010 XDP hFib, Q, rep1 XDP hFib, Q,
GSM7977011 XDP hFib, Q, rep2 XDP hFib, Q,
GSM7977012 Ctrl hFib, NT, rep1 Ctrl hFib, NT,
GSM7977013 Ctrl hFib, NT, rep2 Ctrl hFib, NT,
GSM7977014 Ctrl hFib, B19, rep1 Ctrl hFib, B19,
GSM7977015 Ctrl hFib, B19, rep2 Ctrl hFib, B19,
GSM7977016 Ctrl hFib, Q, rep1 Ctrl hFib, Q,
GSM7977017 Ctrl hFib, Q, rep2 Ctrl hFib, Q,
GSM8398191 Ctrl NPCs, NT, rep3 Ctrl NPCs, NT,
GSM8398192 Ctrl NPCs, B19, rep3 Ctrl NPCs, B19,
GSM8398193 Ctrl NPCs, Q, rep3 Ctrl NPCs, Q,
GSM8398194 XDP NPCs, NT, rep1 XDP NPCs, NT,
GSM8398195 XDP NPCs, NT, rep2 XDP NPCs, NT,
GSM8398196 XDP NPCs, NT, rep3 XDP NPCs, NT,
GSM8398197 XDP NPCs, B19, rep1 XDP NPCs, B19,
GSM8398198 XDP NPCs, B19, rep2 XDP NPCs, B19,
GSM8398199 XDP NPCs, B19, rep3 XDP NPCs, B19,
GSM8398200 XDP NPCs, Q, rep1 XDP NPCs, Q,
GSM8398201 XDP NPCs, Q, rep2 XDP NPCs, Q,
GSM8398202 XDP NPCs, Q, rep3 XDP NPCs, Q,
GSM8398203 NMC hFib, NT, rep3 NMC hFib, NT,
GSM8398204 NMC hFib, B19, rep3 NMC hFib, B19,
GSM8398205 NMC hFib, Q, rep3 NMC hFib, Q,
GSM8398206 XDP hFib, NT, rep3 XDP hFib, NT,

+ 23 more — browse all 63 samples with per-sample file links →

Datasets on a similar topic

GSE250295 G-quadruplexes within the SVA retrotransposon modulate TAF1 gene expression in X-linked Dystonia Parkinsonism 69 samples shares taf1, sva, retrotransposon, g-quadruplexes, parkinsonism, modulate, x-linked, dystonia
GSE250291 G-quadruplexes within the SVA retrotransposon modulate TAF1 gene expression in X-linked Dystonia Parkinsonism [ChIP-seq] 6 samples shares taf1, sva, retrotransposon, g-quadruplexes, parkinsonism, modulate, x-linked, dystonia
GSE289534 A hexamer tandem repeat RNA embedded within an SVA retrotransposon drives R-loop formation and neurodegeneration 41 samples shares sva, retrotransposon
GSE275247 TAF1D promotes tumorigenesis and metastasis by activating PI3K/AKT/mTOR signaling in clear cell renal cell carcinoma 9 samples shares taf1
GSE289670 The effect of PROTAC-mediated depletion of TAF1 on gene expression 6 samples shares taf1
GSE198601 Overexpression of RNA polymerase I specific SL1 component TAF1C induces cancer-specific gene expression in BEAS-2B cells 10 samples shares taf1
GSE283485 G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome [RNA-seq] 24 samples shares g-quadruplexes
GSE247721 Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model [RTE RNA-seq] 24 samples shares retrotransposon

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