Gene Regulatory Network-Driven Drug Repurposing Identifies Anti-Atherosclerotic Properties of Auranofin.
RNA-seq (gene expression) · human · 21 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
- 21 samples: 6 conditions, mostly with about 4 replicates eachGroups 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.
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 GSE293699_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 PRJNA1246056 and SRA study SRP576225. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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.
- GSM8888679 Western Diet 1 Western Diet
- GSM8888680 Western Diet 2 Western Diet
- GSM8888681 Western Diet 3 Western Diet
- GSM8888682 Western Diet 4 Western Diet
- GSM8888683 Western Diet 5 Western Diet
- GSM8888684 Western Diet+atorvastatin 10 mg/kg/day 1 Western Diet+atorvastat…
- GSM8888685 Western Diet+atorvastatin 10 mg/kg/day 2 Western Diet+atorvastat…
- GSM8888686 Western Diet+atorvastatin 10 mg/kg/day 3 Western Diet+atorvastat…
- GSM8888687 Western Diet+auranofin 3 + atoravaststin 10 mg/kg/day 1 Western Diet+auranofin …
- GSM8888688 Western Diet+auranofin 3 + atoravaststin 10 mg/kg/day 2 Western Diet+auranofin …
- GSM8888689 Western Diet+auranofin 3 mg/kg/day 1 Western Diet+auranofin …
- GSM8888690 Western Diet+auranofin 3 mg/kg/day 2 Western Diet+auranofin …
- GSM8888691 Western Diet+auranofin 3 mg/kg/day 3 Western Diet+auranofin …
- GSM8888692 FCs+DMSO 1 FCs+DMSO
- GSM8888693 FCs+DMSO 2 FCs+DMSO
- GSM8888694 FCs+DMSO 3 FCs+DMSO
- GSM8888695 FCs+DMSO 4 FCs+DMSO
- GSM8888696 FCs+AF 0.5uM 1 FCs+AF 0.5uM
- GSM8888697 FCs+AF 0.5uM 2 FCs+AF 0.5uM
- GSM8888698 FCs+AF 0.5uM 3 FCs+AF 0.5uM
- GSM8888699 FCs+AF 0.5uM 4 FCs+AF 0.5uM
- GSE292302 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: RNA-seq 42 samples shares regulatory
- GSE271871 A leiomodin 2 neonatal dilated cardiomyopathy causing mutation results inaltered actin-regulatory gene signatures andcardiomyocyte dysfunction 42 samples shares regulatory
- GSE97179 Single Cell Methylome Signatures Reveal Distinct Neuronal Populations and Regulatory Elements in the Mammalian Cortex 6172 samples shares regulatory
- GSE315628 Single-cell data for FGFR3-driven gene regulatory network analysis reveals a pro-tumoral role for p63 in luminal bladder tumors 6 samples shares regulatory
- GSE253163 Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_RNA_with_blocking] 1 samples shares regulatory
- GSE290623 Opposing functions of distinct regulatory T cell subsets in colorectal cancer 142 samples shares regulatory
- GSE286473 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry 95 samples shares regulatory
- GSE292300 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: ChIP-seq 76 samples shares regulatory
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.