Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model [iPS-VEC 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-VEC, oxLDL, neg, vs 3 × WS, iPS-VEC, oxLDL, neg, vs 3 × Healthy, iPS-VEC, oxLDL, pos, vs 3 × WS, iPS-VEC, 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 GSE247710_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 PRJNA1040194 and SRA study SRP471807. 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.
- GSM7899166 Healthy, iPS-VEC, oxLDL, neg, 1 Healthy, iPS-VEC, oxLDL…
- GSM7899167 Healthy, iPS-VEC, oxLDL, neg, 2 Healthy, iPS-VEC, oxLDL…
- GSM7899168 Healthy, iPS-VEC, oxLDL, neg, 3 Healthy, iPS-VEC, oxLDL…
- GSM7899169 WS, iPS-VEC, oxLDL, neg,1 WS, iPS-VEC, oxLDL, neg,
- GSM7899170 WS, iPS-VEC, oxLDL, neg, 2 WS, iPS-VEC, oxLDL, neg,
- GSM7899171 WS, iPS-VEC, oxLDL, neg, 3 WS, iPS-VEC, oxLDL, neg,
- GSM7899172 Healthy, iPS-VEC, oxLDL, pos, 1 Healthy, iPS-VEC, oxLDL…
- GSM7899173 Healthy, iPS-VEC, oxLDL, pos, 2 Healthy, iPS-VEC, oxLDL…
- GSM7899174 Healthy, iPS-VEC, oxLDL, pos, 3 Healthy, iPS-VEC, oxLDL…
- GSM7899175 WS, iPS-VEC, oxLDL, pos,1 WS, iPS-VEC, oxLDL, pos,
- GSM7899176 WS, iPS-VEC, oxLDL, pos, 2 WS, iPS-VEC, oxLDL, pos,
- GSM7899177 WS, iPS-VEC, oxLDL, pos, 3 WS, iPS-VEC, oxLDL, pos,
- 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
- GSE247718 Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model [VSMC 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
- GSE272294 Decoding the immune checkpoint signatures in human atherosclerosis: implications of type 2 diabetes and lipid-lowering intervention [human PBMC scRNA-Seq] 24 samples shares atherosclerosis, rna-seq
- GSE282042 RNA-seq analysis of human monocytes in patients with and without coronary atherosclerosis 20 samples shares atherosclerosis, 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.