One deficiency, different outcomes: Succinate dehydrogenase loss in chromaffin cell vs. fibroblast models of paraganglioma
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × iMEF_WT vs 3 × iMEF_SDH vs 3 × imCC_WT vs 3 × imCC_SDHGroups 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
- Similar deficiencies, different outcomes: succinate dehydrogenase loss in adrenal medulla vs. fibroblast cell culture models of paragangliomaCancer & metabolism · 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 GSE263778_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 PRJNA1099228 and SRA study SRP501210. 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.
- GSM8198436 iMEF_WT1 iMEF_WT
- GSM8198437 iMEF_WT2 iMEF_WT
- GSM8198438 iMEF_WT3 iMEF_WT
- GSM8198439 iMEF_SDH1 iMEF_SDH
- GSM8198440 iMEF_SDH2 iMEF_SDH
- GSM8198441 iMEF_SDH3 iMEF_SDH
- GSM8198442 imCC_WT1 imCC_WT
- GSM8198443 imCC_WT2 imCC_WT
- GSM8198444 imCC_WT3 imCC_WT
- GSM8198445 imCC_SDH1 imCC_SDH
- GSM8198446 imCC_SDH2 imCC_SDH
- GSM8198447 imCC_SDH3 imCC_SDH
- GSE306049 Atf3 Deficiency Promotes Mesodermal Commitment and Enhances Endothelial Differentiation in Embryonic Stem Cells 24 samples shares deficiency, different
- GSE267771 KMT2C Deficiency Drives Luminal Transdifferentiation into Double-Negative Prostate Cancer and Sensitizes to Fatty Acid Synthase Inhibition [RNA-Seq] 22 samples shares deficiency, different
- GSE296977 H4K16 acylations fine-tune transcriptional response to short-chain acyl-CoA dehydrogenase deficiency (ChIP-seq) 24 samples shares dehydrogenase, deficiency
- GSE243060 Multi-organ Transcriptome Atlas of a Mouse Model of Relative Energy Deficiency in Sport (REDs) 419 samples shares deficiency
- GSE254229 ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits in mice 141 samples shares deficiency
- GSE267786 Impact of SLC15A4, TASL and TASL2(Gm6377) deficiency on endolysosomal TLR7 and TLR9 responses 95 samples shares deficiency
- GSE260623 Germline ELP1 deficiency sensitizes cerebellar granule neuron progenitors to SHH medulloblastoma [bulkRNA] 91 samples shares deficiency
- GSE281404 Deficiency of the palmitoyl acyltransferase ZDHHC7 modulates gene expression in mice after a mild chronic stress paradigm 80 samples shares deficiency
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.