G-quadruplexes within the SVA retrotransposon modulate TAF1 gene expression in X-linked Dystonia Parkinsonism
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 69 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 69 samples: 24 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
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 GSE250295_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1053312 and SRA study SRP478259. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 69 samples.
How we read this: 24 replicated groups read from 69 sample titles; they account for 69 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.
- GSM7976954 NMC_A2_G4ChIPseq_rep01 NMC_A2_G4ChIPseq
- GSM7976955 XDP_B2_G4ChIPseq_rep01 XDP_B2_G4ChIPseq
- GSM7976956 ctrl_E2_G4ChIPseq_rep01 ctrl_E2_G4ChIPseq
- GSM7976957 NMC_A2_G4ChIPseq_rep02 NMC_A2_G4ChIPseq
- GSM7976958 XDP_B2_G4ChIPseq_rep02 XDP_B2_G4ChIPseq
- GSM7976959 ctrl_E2_G4ChIPseq_rep02 ctrl_E2_G4ChIPseq
- 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,
+ 29 more — browse all 69 samples with per-sample file links →
- GSE250293 G-quadruplexes within the SVA retrotransposon modulate TAF1 gene expression in X-linked Dystonia Parkinsonism [RNA-Seq] 63 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
- GSE198601 Overexpression of RNA polymerase I specific SL1 component TAF1C induces cancer-specific gene expression in BEAS-2B cells 10 samples shares taf1
- 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
- GSE247722 Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model 97 samples shares retrotransposon
- GSE296647 Indirect identification of genomic G-quadruplexes via a small protein probe that specifically recognizes C-rich single-stranded DNA 24 samples shares g-quadruplexes
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.