List of species

• Human
• Mouse
• Rat
• Zebrafish
• Arabidopsis thaliana
• E.Coli
• Yeast

ISMARA analysis examples:

Human (assembly hg38)

• Epithelial-Mesenchymal Transition, human (Scheel, 2011)
  • Epithelial-Mesenchymal Transition averaged across subpopulations, human (Scheel, 2011)

Human (assembly hg19)

Transcriptional response to SARS-CoV-2 infection (GSE147507)

This analysis was conducted by Dr. Andreas Gruber for covid-19-bh20 biohackathon

• All samples
• All samples, averaged replicates
• NHBE cells infected with SARS-CoV-2 plus mock control
• NHBE cells infected with SARS-CoV-2 plus mock control, averaged replicates
• A549 cells infected with SARS-CoV-2 plus mock control
• A549 cells infected with SARS-CoV-2 plus mock control, averaged replicates
• A549 cells infected with RSV (respiratory syncytial virus) plus mock control
• A549 cells infected with RSV (respiratory syncytial virus) plus mock control, averaged replicates
• A549 cells infected with IAV (influenza A virus) plus mock control
• A549 cells infected with IAV (influenza A virus) plus mock control, averaged replicates

Rat (assembly rn6)

• A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages. (GSE53960)
• Hypoxia transcriptome sequencing of rat brain. (GSE49485)

Zebrafish (assembly dr11)

• Sequencing zebrafish transcriptome at different developmental stages. (PRJEB1986)
• RNA-sequencing project for zebrafish embryo and larva development. (GSE45706)
• Tissue specific transcriptome profiling of zebrafish. (PRJNA207719)
• RNAseq of wild type zebrafish germline (ovary, oocyte, testis). (GSE111882)
• Age associated transcriptome analysis in 5 tissues of zebrafish. (PRJDB7713)

Arabidopsis thaliana (assembly Araport11)

• Time-course of wild-type Arabidopsis leaf (GSE43616)
• Vernalization in Arabidopsis thaliana (GSE130291)

Yeast (sacSer2)

• A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism (GSE151185)

E.Coli (based on RegulonDB, release 2017)

• Plasticity of transcriptional regulation under antibiotic stress. (GSE55662)
• Regulatory changes under long-term starvation (GSE67402)
• Transcriptome analysis of E. coli grown aerobically and anaerobically (GSE80451)