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List of species

• Human
• SARS-CoV-2
• Mouse
• Rat
• Zebrafish
• Arabidopsis thaliana
• E.Coli
• Yeast
• Epi-Mara

Additional example results of ISMARA analysis

Human (hg38)

• Illumina Body Map 2 (GSE30611)
  • Illumina Body Map 2, averaged replicates
  • Illumina Body Map 2, young vs old
• GNF SymAtlas + NCI-60 cancer cell lines, human (Su, 2004; Ross, 2000)
  • GNF SymAtlas + NCI-60 cancer cell lines, comparison of cancers vs non-cancers, human (Su, 2004; Ross, 2000)
• Inflammatory response time course, HUVEC (Wada et al, 2009),
• Mucociliary differentiation, bronchial epithelial cells, human (Ross 2007)
• Epithelial-Mesenchymal Transition, human (Scheel, 2011)
  • Epithelial-Mesenchymal Transition averaged across subpopulations, human (Scheel, 2011)

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

Mouse (mm39)

• Comprehensive Mouse Transcriptomic BodyMap (PRJNA375882)
• Dynamics of the Mouse Liver (Renaud 2014) (GSE58827)
  • Dynamics of the Mouse Liver, averaged replicates (Renaud 2014)

Rat (rn6)

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

Zebrafish (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 (Araport11)

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

E.Coli (RegulonDB 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)

Yeast (sacSer2)

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

Epi-Mara results:

• Arnold, Schöler et al. "Modeling of epigenome dynamics during differentiation reveals REST as a mediator of Polycomb targeting in neuronal progenitors."