Effect of coixenolide on pancreatic tumor gene expression in HFD and CD groups
RNA-seq (gene expression) · mouse · 13 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
- 13 samples: 4 × HFDcoixenolide vs 3 × CDCtrl vs 3 × CDcoixenolide vs 3 × HFDCtrlGroups 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 GSE302413_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 PRJNA1290360 and SRA study SRP600257. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 13 samples.
How we read this: 4 replicated groups read from 13 sample titles; they account for 13 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.
- GSM9103703 CDCtrl1 CDCtrl
- GSM9103704 CDCtrl2 CDCtrl
- GSM9103705 CDCtrl3 CDCtrl
- GSM9103706 CDcoixenolide1 CDcoixenolide
- GSM9103707 CDcoixenolide2 CDcoixenolide
- GSM9103708 CDcoixenolide3 CDcoixenolide
- GSM9103709 HFDCtrl1 HFDCtrl
- GSM9103710 HFDCtrl2 HFDCtrl
- GSM9103711 HFDCtrl3 HFDCtrl
- GSM9103712 HFDcoixenolide1 HFDcoixenolide
- GSM9103713 HFDcoixenolide2 HFDcoixenolide
- GSM9103714 HFDcoixenolide3 HFDcoixenolide
- GSM9103715 HFDcoixenolide4 HFDcoixenolide
- GSE217560 Gene expression profile at single cell level of bone marrow and brain cells from young adult and aged mouse after chewing diet (CD) and long-term high-fat diet (HFD) feeding 8 samples shares hfd
- GSE288503 Secreted chemokines and transcriptomic analyses reveal diverse inflammatory and degenerative processes in the intervertebral disc of the STZ-HFD mouse model of Type 2 diabetes 14 samples shares hfd
- GSE302874 HFD-inducued metabolic syndrome is promoted by JNK7b isoform. 69 samples shares hfd
- GSE254704 Skeletal muscle cystathionine γ-lyase deficiency promotes obesity and insulin resistance and results in hyperglycemia and skeletal muscle injury upon HFD in mice 32 samples shares hfd
- GSE286167 Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_HFD] 23 samples shares hfd
- GSE244342 Activated-ATF6α is an ER stress-inducing oncoprotein metabolically restricting immunosurveillance [bulk RNA-seq of TG-AAV-GFP/CRE, DEN/HFD] 16 samples shares hfd
- GSE293937 scRNA-seq of fasted or 1 hour refed mouse hypothalamus after 6 weeks of HFD 13 samples shares hfd
- GSE299487 LY6D Identifies Persistent Tumor-Initiating Cells Driving Pancreatic Tumorigenesis [scRNA-seq] 12 samples shares pancreatic
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.