inst/extdata/ex_datasets.md

In OceaneCsn/DIANE: DIANE

Ready to explore RNA-Seq datasets

RNA-Seq expriments from different published studies are gathered here. Most of them were found in the Expression Atlas.

You can download them to see the expected file format in DIANE for your organism, and/or upload them in the app direclty, without any further formatting needed.

Make sure to disable the “Demo data” option in the Import data tab, and then to chose the correct organism before uploading. All of the files are comma separated.

• Left ventricular implant devices in humans

Mitchell A, Guan W, Staggs R, et al. Identification of differentially expressed transcripts and pathways in blood one week and six months following implant of left ventricular assist devices. Plos one. 2013 ;8(10):e77951. DOI: 10.1371/journal.pone.0077951.

Publication | Expression Atlas | Download expression file

• Effect of intermitent fasting on mouse

Ng GY, Kang SW, Kim J, et al. Genome-Wide Transcriptome Analysis Reveals Intermittent Fasting-Induced Metabolic Rewiring in the Liver. Dose-response : a Publication of International Hormesis Society. 2019 Jul-Sep;17(3):1559325819876780. DOI: 10.1177/1559325819876780.

Publication | Expression Atlas | Download expression file

• Drosophilia eye development and gene dosage of DeIF6

Stefano Biffo,Arianna Russo,Cristina Cheroni,Piera Calamita,Roberta Alfieri (2019). RNA-seq analysis of gene expression associated to altered gene dosage of DeIF6 during eye development in Drosophila melanogaster, arrayexpress-repository, V1.

Transcriptomes for eye disc and retina, either for genotypes GMR/+ (wild type phenotype) or GMR>DeIF6 (DeIF6 overexpression phenotype).

Data Publication | Expression Atlas | Download expression file

• Cluster root density in white Lupin

Spatial transcriptomic dataset of lateral root and increasing proteoid root density (BPMP, Plasticity team).

Publication | White lupin website | Download expression file

• Three bacterial diets for C. elegans

RNAseq of young adult Caenorhabditis elegans animals fed on three different bacterial diets, E. coli OP50, B. subtilis PXN21 and a mixture of both.

Goya ME, Xue F, Sampedro-Torres-Quevedo C, et al. Probiotic Bacillus subtilis Protects against α-Synuclein Aggregation in C. elegans. Cell Rep. 2020;30(2):367-380.e7. doi:10.1016/j.celrep.2019.12.078

Publication | Expression Atlas | Download expression file

• Escherichia coli's transcriptome after anaerobic-aerobic transition

von Wulffen J, RecogNice-Team., Sawodny O, Feuer R. Transition of an Anaerobic Escherichia coli Culture to Aerobiosis: Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis. PLoS One 2016;11(7):e0158711. PMID: 27384956

Publication | Gene Accession Omnibus entry | Download expression file

Enjoy your transcriptome exploration!

OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.