Studies

A minimal metadata template for high content screening experiments in microscopy. The template is compliant with REMBI (Recommended Metadata for Biological Images) and the ISA framework (Investigations, Studies and Assays).

Here you will find guidelines for filling in MIHCSME metadata templates, as well as examples of published HCS studies that use MIHCSME.

This study describes the results of a survey on enrichment analysis tool usage and provenance reporting for a corpus of SARS-CoV2 data.

This study investigates the citations of reproducible vs. not reproducible papers and is based on 328 published models, classified by Tiwari et al. based on their reproducibility are analyzed in this study. Hypothese testing is performed using a flexible Bayesian approach for a complete assessment of posteriors. The approach handels outliers via a non-central t distribution. Results show that reproducible papers are significantly more citet between 2013 and 2020, i.e. 10 years after the introduction ...

This study contains the singele nuclei data analysis part of the Bl6 and Rag2del comparison. Here, we used Seurat, harmony, and monocle for an in-depth analysis.

Short Name: DiNAR Title: DiNAR analyses of SxP DE data Description: DiNAR visualisation of SxPv1.0 and SxPv1.2 expressoin data in either PIS or CKN networks. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: Gibberelin_treatment Title: GA3 treatment of SxPs Description: SxP lines were treated with 3 different GA3 concentrations (1, 10 and 100 micromolar) and control solution. WT Nb plants were used for control. From v1.0 T3, low producing line 5_2_5 and high producing line 5_1_7 were used and from v1.2 T2 lines 4_1 and 4_3. Treatment was done for 5 consecutive weeks, once per week with spraying the leaves. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution ...

Short Name: P4_SxP10-newG-DE Title: SxPv1.0 RNA-seq analysis using the new Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the not yet published now high quality genome of Nicotiana benthamiana from the Newcotiana project. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_SxP10-oldG-DE Title: SxPv1.0 RNA-seq analysis using old Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the published (old) genome of Nicotiana benthamiana. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: No

Short Name: P4_SxP1012-finalG Title: Reanalysis of SxP Illumina reads with Nb genome V3.5 Description: * Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_SxP12-newG-DE Title: Gene expression analysis of Sxp 1.2 Description: exp4 in phenodata Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P1_SPv10T2andT3 Title: Characterization of SPv1.0 plants of the T2 and T3 generations Description: Plants of the SxP v1 second and third generation were grown in the greenhouse and leaf samples were collected for analysing their metabolome (via GC-MS) and transcriptome (via RNA-seq). Phenotypic data such as plant height was also recorded. Raw Data: pISA Study creation date: 2018-11-09 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative Commons Attribution ...

Short Name: P1_SPv1TransientExp Title: Transient expression in Nicotiana benthamiana leaves of constructs for SPv1 Description: The constructs for stable transformation of SPv1.X versions were tested transiently via agroinfiltration of Nicotiana benthamiana leaves. Pheromone content was analysed via GC-MS Raw Data: pISA Study creation date: 2019-12-08 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to ...

Short Name: P1_SxPAltAcTransferases Title: Study of alternative acetyltransferases for future SxP versions Description: Study of transient expression of different acetyltransferase genes responsible of the catalysis of the conversion of Z11-16OH into Z11-16OAc, assayed in Nicotiana benthamiana WT plants. Raw Data: pISA Study creation date: 2021-11-25 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: ...

Short Name: P1_SxPv10vsSxP12 Title: Comparison between SxPv1.0 and SxPv1.2 Description: Volatilome characterization of SxPv1.0 T3 plants, SxPv1.2 T1 plants and WT plants. Raw Data: pISA Study creation date: 2020-11-01 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: SxPv12T2Analysis Title: Analysis of second generation of SxPv1.2 plants Description: Characterization of SxPv1.2 T2 plants. Raw Data: pISA Study creation date: 2021-12-09 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes Institutions involved: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Spain; Institute of Agrochemistry and Food Technology (IATA), Spain; The ...

Short Name: CoExpNetViz Title: CoExpNetViz Description: Coexpression analyses with CoExpNetViz tool. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation files _I_T21_SXPsysbio

Short Name: P1_SPv10T0andT1 Title: Characterization of SPv1.0 plants of the T0 and T1 generations Description: SP v1.0 plants were generated and studied (T0), as well as the first generation (T1). Plants were grown in the greenhouse and leaf samples were collected for analysing their metabolome (via GC-MS). Phenotypic data such as plant height was also recorded. Raw Data: pISA Study creation date: 2021-11-01 pISA Study creator: AlfredoQR Principal investigator: Diego Orzaez License: Creative ...

Development of an effective tuberculosis (TB) vaccine has suffered from an incomplete understanding of the correlates of protection against Mycobacterium tuberculosis (Mtb). Intravenous (i.v.) vaccination with Bacille Calmette–Guérin (BCG) provides nearly complete protection against TB in rhesus macaques, but the antibody response it elicits remains incompletely defined. Here we show that i.v. BCG drives superior antibody responses in the plasma and the lungs of rhesus macaques compared to ...

To allow detailed visual analysis of the overall system and its parts, we used a customised version of our Vanted add-on LMME (Large Metabolic Model Explorer) to construct an overview graph showing one node per pathway and the respective interconnecting species. We performed a comprehensive analysis of node centralities on two levels: on the level of the individual pathways as well as on the level of an aggregated network which is composed of the individual pathways. This allows detailed ...

An exploration on gene expression data was carried out on single-cell RNAseq analyses of bronchoalveolar lavages from nine COVID-19 patients, three moderate cases, one severe case and five critical cases (GSE145826) (doi: 10.1038/s41591-020-0901-9). To these data, single-cell RNA-sequencing from one COVID-19 lung biopsy, ~10 weeks after initial infection was added to represent persistent severe COVID19 patient group (3 weeks after symptom onset) (GSE163919). For this analysis, the epithelial cell ...

Modelling and experiments for FMv2 components.

Simulations, parameter sensitivity analysis etc. for FMv2

Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)

Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)

Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)