Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model [VSMC 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: 3 × Healthy, iPS-VSMC, oxLDL, neg, vs 3 × WS, iPS-VSMC, oxLDL, neg, vs 3 × Healthy, iPS-VSMC, oxLDL, pos, vs 3 × WS, iPS-VSMC, oxLDL, pos,Groups 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
- Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis modelNature communications · 2024
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 GSE247718_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 PRJNA1040213 and SRA study SRP471808. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 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.
- GSM7899244 Healthy, iPS-VSMC, oxLDL, neg, 1 Healthy, iPS-VSMC, oxLD…
- GSM7899245 Healthy, iPS-VSMC, oxLDL, neg, 2 Healthy, iPS-VSMC, oxLD…
- GSM7899246 Healthy, iPS-VSMC, oxLDL, neg, 3 Healthy, iPS-VSMC, oxLD…
- GSM7899247 WS, iPS-VSMC, oxLDL, neg, 1 WS, iPS-VSMC, oxLDL, ne…
- GSM7899248 WS, iPS-VSMC, oxLDL, neg, 2 WS, iPS-VSMC, oxLDL, ne…
- GSM7899249 WS, iPS-VSMC, oxLDL, neg, 3 WS, iPS-VSMC, oxLDL, ne…
- GSM7899250 Healthy, iPS-VSMC, oxLDL, pos, 1 Healthy, iPS-VSMC, oxLD…
- GSM7899251 Healthy, iPS-VSMC, oxLDL, pos, 2 Healthy, iPS-VSMC, oxLD…
- GSM7899252 Healthy, iPS-VSMC, oxLDL, pos, 3 Healthy, iPS-VSMC, oxLD…
- GSM7899253 WS, iPS-VSMC, oxLDL, pos, 1 WS, iPS-VSMC, oxLDL, po…
- GSM7899254 WS, iPS-VSMC, oxLDL, pos, 2 WS, iPS-VSMC, oxLDL, po…
- GSM7899255 WS, iPS-VSMC, oxLDL, pos, 3 WS, iPS-VSMC, oxLDL, po…
- GSE247721 Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model [RTE RNA-seq] 24 samples shares interferon-dependent, retrotransposons, syndrome-derived, atherosclerosis, macrophages, trigger, rna-seq
- GSE247717 Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model [iPS macrophage RNA-seq] 20 samples shares interferon-dependent, retrotransposons, syndrome-derived, atherosclerosis, macrophages, trigger, rna-seq
- GSE247710 Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model [iPS-VEC RNA-seq] 12 samples shares interferon-dependent, retrotransposons, syndrome-derived, atherosclerosis, macrophages, trigger, rna-seq
- GSE247722 Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model 97 samples shares interferon-dependent, retrotransposons, syndrome-derived, atherosclerosis, macrophages, trigger
- GSE247716 Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model [iPS ATAC-seq] 20 samples shares interferon-dependent, retrotransposons, syndrome-derived, atherosclerosis, macrophages, trigger
- GSE247705 Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model [H3K9me3 ChIP-seq] 9 samples shares interferon-dependent, retrotransposons, syndrome-derived, atherosclerosis, macrophages, trigger
- GSE292899 Loss of H3K9me3 maintenance leads in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons [Bulk RNA-seq] 20 samples shares retrotransposons, rna-seq
- GSE95516 Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [RNA-Seq Human] 8 samples shares retrotransposons, rna-seq
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.