Studies
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Meng Sun*, Jolie M. Phan*, Nathan S. Kieswetter, Krystle K.Q. Yu, Malisa T. Smith, Huang Huang, Sanjana Gupta, Gerlinde Obermoser, Holden Terry Maecker, Akshaya Krishnan, Neha Gupta, Mary Rieck, Peter Acs, Mustafa Ghanizada, Shin-Heng Chiou, Purvesh Khatri, W. Henry Boom, Thomas R. Hawn, Catherine M. Stein, Harriet Mayanja-Kizza, Mark M. Davis*, Chetan Seshadri*
Abstract: A subset of individuals with a high probability of exposure to M. tuberculosis (M.tb) ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata
Thiel BA, Worodria W, Nalukwago S, Nsereko M, Sanyu I, Rejani L, Zawedde J, Canaday DH, Stein CM, Chervenak KA, Malone LL, Kiyemba R, Silver RF, Johnson JL, Mayanja-Kizza H, Boom WH. Immune cells in bronchoalveolar lavage fluid of Ugandan adults who resist versus those who develop latent Mycobacterium tuberculosis infection. PLoS One. 2021 Apr 9;16(4):e0249477. doi: 10.1371/journal.pone.0249477. PMID: 33836031; PMCID: PMC8034721.
Abstract: ...
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: Flow Cytometry Processing – Data Attached, Flow Cytometry – Data Linked, Patient Visit – Metadata, Tissue Collection - Metadata
Induced fit docking studies of the dinitroaniline parent trifluraline and the newly designed dinitroaniline-etherphospholipid hybrids against different potential binding sites in monomeric and multimeric kinetoplastid tubulin receptors.
Submitter: Ina Poehner
Investigation: Antiparasitic dinitroaniline-ether phospholipid...
Assays: Induced-fit docking studies, Preparation of multimeric tubulin docking receptors
This study includes the experimental data for model validation and the model predictions of that data set.
Submitter: Dawie van Niekerk
Investigation: Glucose metabolism in Plasmodium falciparum inf...
Assays: Inhibition of glycolytic flux, Metabolic control analysis
This study includes the experimental data for model validation and the model predictions of that data set.
Submitter: Dawie van Niekerk
Investigation: Glucose metabolism in Plasmodium falciparum inf...
Assays: Flux vs external glucose, Flux vs parasitaemia, GLC incubation, Stage specific fluxes, Steady-state
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: Single Cell Sequencing Analysis – Data Linked, Single Cell Sequencing – Data Linked, Tissue Extraction – Metadata
Haosheng Feng, Shao-Xiong Lennon Luo, Robert G Croy, John M. Essigmann, Timothy M. Swager
https://doi.org/10.1039/D2DT03848J
Cu(I) from tetrakis(acetonitrile)copper(I) hexafluorophosphate ([Cu(MeCN)4]PF6) was complexed with five structurally related phosphines containing N-heterocycles. The interactions between the resulting complexes and some N-nitrosamines were studied using X-ray crystallography as well as emission spectroscopy. Upon complexation, three ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: Absorption and Emission Spectroscopy - Data Linked, Absorption and Emission Spectroscopy Analysis - Data Linked, Chemical Synthesis - Metadata, Crystallography - Data Linked, Electron Paramagnetic Resonance - Data Linked, High Resolution Mass Spectra - Data Linked, High Resolution Mass Spectra Analysis - Data Linked, Nuclear Magnetic Resonance Spectroscopy - Data Linked, Nuclear Magnetic Resonance Spectroscopy Analysis - Data Linked, X-ray Photoelectron Spectroscopy - Data Linked
Amanda L. Armijo, Pennapa Thongaram, Bogdan I. Fedeles, Judy Yau, Jennifer E Kay, Joshua J. Corrigan, Marisa Chancharoen, Supawadee Chawanthayatham, Leona D. Samson, Sebastian E. Carrasco, Bevin P. Engelward, James G. Fox, Robert G. Croy & John M. Essigmann
DNA-methylating environmental carcinogens such as N-nitrosodimethylamine (NDMA) and certain alkylators used in chemotherapy form O6-methylguanine (m6G) as a functionally critical intermediate. NDMA ...
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: Kinetics Minireviews, Models
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: ACAD activity partitioning, HepG2 oxygen consumption, Whole-body ketogenic flux
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: Comparing acyl-CoA dehydrogenase deficiencies, MCADD patient personalised modelling, MCADD rescue titration, Metabolic control analysis, Predicting urinary acylcarnitines under metabolic decompensation.
Sequence and electrostatic potential analyses to identify sites in tubulins that differ between dinitroaniline-sensitive and dinitroaniline-resistant species.
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.
Submitter: Rohola Hosseini
Investigation: Minimal Information for High Content Screening ...
Assays: General MIHCSME template, MIHCSME template example for "Integration of biological data by kernels ..., MIHCSME template example for "Uncovering the signaling landscape control..., MIHCSME template example for compound screen on HepG2 CHOP-GFP reporter ..., MIHCSME template example for “Temporal single cell cellular stress respo...
This study describes the results of a survey on enrichment analysis tool usage and provenance reporting for a corpus of SARS-CoV2 data.
Submitter: Yi Chen
Investigation: FAIR Functional Enrichment: Assessing and Model...
Assays: FAIR Functional Enrichment
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 ...
Submitter: Sebastian Höpfl
Investigation: 1 hidden item
Assays: Statistical analysis and BEST method of Kruschke for python applied on c...
Submitter: Uta Dahmen
Investigation: 1 hidden item
Assays: Animal experiment and Pharmacokinetics data, Bayesian uncertainty quantification, Hematoxylin-Eosin (HE) staining, Immunohistochemistry _ CYP1A2, Immunohistochemistry _ CYP2D6, Immunohistochemistry _ CYP2E1, Immunohistochemistry _ CYP3A4, SteaPk-data Histology Quant., CYP activity, Protein, TG, AUC
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.
Submitter: Markus Wolfien
Investigation: Disparate immune responses lead to varied outco...
Submitter: Meina Neumann-Schaal
Investigation: Systems biology investigation of aromatic compo...
Assays: CoA LC/MS Data, Cultivation for multi-OMICS, Proteomic data, Transcriptomic data, non-volatile metabolites GC/MS
Submitter: Meina Neumann-Schaal
Investigation: Systems biology investigation of aromatic compo...
Assays: EbN1 Genome re-annotation
Submitter: Meina Neumann-Schaal
Investigation: Systems biology investigation of aromatic compo...
Assays: Metabolic modeling of EbN1, Scenario files for Metano metabolic modeling
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
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_CKN-DiNAR, _A_CKN_NbL35-DiNAR, _A_PIS-DiNAR, _A_PIS-SxPv12-DiNAR, _A_PIS_NbL35-DiNAR, _S_P4_DiNAR-files
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 ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
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
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_toNewGenome-CLC-mapping, _A_02_limmavoomDE-R, _A_02a_limmavoomDEbylines-R, _A_03_NewGenome-MapMan, _A_04_GSEA-Stat, _A_05_Phenotype_analysis-Stat, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _S_P4_SxP10-newG-DE-files
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
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_00_SxP_photos-phenotyping, _A_01_RNA1-RNAisol, _A_02_FastQC-bioinfo, _A_03_mapping-CLC, _A_03a_mapping2-STAR, _A_04_Mercator-bioinfo, _A_05_DEstat-R, _A_05a_DEstat2-R, _A_05b_DElow-wt-R, _A_06_MapMan-bioinfo, _A_07_transgenes-CLC, _S_P4_SxP10-oldG-DE-files
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
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_SxPv12_fastq-QC, _A_02_SxPv12_mapping-CLC, _A_03_SxPv12_limmavoom_DE-R, _A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA, _S_P4_SxP12-newG-DE-files
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 ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SPv10T2Analysis-GCMS, _A_SPv10T3Analysis-GCMS, _A_SPv10_phenotyping-Images, _S_P1_SPv10T2andT3-files
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 ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SPv10EaDActAnalysis-GCMS, _A_TransientSPv11andSPv12-GCMS, _S_P1_SPv1TransientExp-files