Flora D'Anna
SEEK ID: https://datahub-test.elixir-belgium.org/people/3
Locations:
United Kingdom
, 
Belgium
, 
Sweden
ORCID: Not specified
Joined: 18th Jul 2022
Expertise: Not specified
Tools: Not specified
Roles
Admin
Project administrator
- ISA ENA export
- testing template created by user in SP
- Second project
- Genetic properties of the MAGIC maize population
- WP1 - Learning techniques fit for industrial biotechnology
- WP2 - Bioprospecting and functional expression of CYPs
- deCYPher Composable Elements
- deCYPher experiments templates
- HoloFood in DataHub
Programme administrator
Their tagsRelated items
This is an example of how multi-omics study can be organised in DataHub. The HoloFood project is used as an example here.
Projects: HoloFood in DataHub
Web page: Not specified
Projects: EGA submissions - H. Granger Lab, Croockshanks' PhD
Web page: Not specified
Projects: Templates - EGA Data Access Committee @ VIB
Web page: Not specified
Data from Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays https://doi.org/10.1186/s13059-015-0716-z
Projects: Genetic properties of the MAGIC maize population
Web page: Not specified
Example
Programme: Example with HoloFood project
Public web page: Not specified
Programme: H. Granger Lab @ VIB
Public web page: Not specified
Programme: EGA Data Access Committee @ VIB
Public web page: Not specified
Programme: H. Potter Lab @ VIB
Public web page: Not specified
Programme: H. Granger Lab @ VIB
Public web page: Not specified
ROR ID: Not specified
Department: Not specified
Country: United Kingdom
City: Not specified
Web page: Not specified
ROR ID: Not specified
Department: Not specified
Country: Belgium
City: Not specified
Web page: Not specified
ROR ID: Not specified
Department: Not specified
Country: Sweden
City: Stockholm
Web page: Not specified
ROR ID: Not specified
Department: Not specified
Country: Not specified
City: Not specified
Web page: Not specified
ROR ID: https://ror.org/03xrhmk39
Department: Not specified
Country: Belgium
City: Ghent
Web page: https://vib.be/
Multi-modal investigation in chickens
WGS, RNAsequencing and genotyping of founders lines
Hologenomic approach to understand the impact of host–microbiota interactions on chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds.
Submitter: Flora D'Anna
Investigation: Multi-omics in chickens
Assays: Chromatography, Library for host transcriptomics, Mass spectrometry, Metabolites extraction, Metabolomics, Transcriptome sequencing, Transcriptomics
Genome-seq_RNAseq_variants of founders lines
Submitter: Flora D'Anna
Investigation: Characterisation of founders lines
Assays: Genome Assembly, Genome Variants, Genome sequencing, Genomic, Genomic variants, Genomic variants, Library preparation, Library preparation, RNA extraction, RNA sequencing, Transcriptomics
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Characterisation of founders lines
Study: Genome-seq_RNAseq_variants
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Characterisation of founders lines
Study: Genome-seq_RNAseq_variants
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Characterisation of founders lines
Study: Genome-seq_RNAseq_variants
Genomic variants
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Characterisation of founders lines
Study: Genome-seq_RNAseq_variants
Library for host transcriptomics
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Multi-omics in chickens
Library construction for HoloFood shotgun chicken transcriptomics
Creator: Flora D'Anna
Submitter: Flora D'Anna
HoloFood chromatography
Creator: Flora D'Anna
Submitter: Flora D'Anna
HoloFood metabolites extraction
Creator: Flora D'Anna
Submitter: Flora D'Anna
Genome assembly protocol
Creator: Flora D'Anna
Submitter: Flora D'Anna
Library preparation was done using the TruSeq RNA Sample Preparation Kit v2 (Illumina). In brief, starting from total RNA the mRNA is purified using polyA selection. Following chemically fragmentation the mRNA is converted into single-stranded cDNA using random hexamer priming. Next, double-stranded cDNA is generated and adapters are ligated.
Creator: Flora D'Anna
Submitter: Flora D'Anna
Abstract (Expand)
Authors: Núria Tous, Sofia Marcos, Farshad Goodarzi Boroojeni, Ana Pérez de Rozas, Jürgen Zentek, Andone Estonba, Dorthe Sandvang, M. Thomas P. Gilbert, Enric Esteve-Garcia, Robert Finn, Antton Alberdi, Joan Tarradas
Date Published: 6th Sep 2022
Publication Type: Peer Review
Abstract (Expand)
Authors: M. Dell'Acqua, D. M. Gatti, G. Pea, F. Cattonaro, F. Coppens, G. Magris, A. L. Hlaing, H. H. Aung, H. Nelissen, J. Baute, E. Frascaroli, G. A. Churchill, D. Inze, M. Morgante, M. E. Pe
Date Published: 11th Sep 2015
Publication Type: Journal Article
'Assay - Data file' Sample Type linked to Assay 'Transcriptome sequencing'.
Input (title) (Registered Sample List) *, nucleic acid sequencing (String) *, Raw Data File (String) *, file_name (String) *, file_type (Controlled Vocabulary - file_type) *, run_accession (String) , fastq_ftp (String) , submitted_bytes (String) , submitted_ftp (String) , bam_ftp (String)
Not specified
'Assay - Material' Sample Type linked to Assay 'Library for host transcriptomics'.
Input (Sample Name) (Registered Sample List) *, protocol (Registered SOP) *, title (String) *, library_name (String) *, design_description (String) *, library_source (Controlled Vocabulary - library_source) *, library_strategy (Controlled Vocabulary - library_strategy) *, library_selection (Controlled Vocabulary - library_selection) *, library_layout (Controlled Vocabulary - library_layout) *, platform (Controlled Vocabulary - platform) *, instrument_model (Controlled Vocabulary - instrument_model) *, experiment accession (String)
Not specified
'Assay - Data file' Sample Type linked to Assay 'Mass spectrometry'.
Input (Labeled Extract Name) (Registered Sample List) *, MS Protocol (String) *, scan polarity (Controlled Vocabulary - deCYPher_MS_scan-polarity) , scan m/z range (String) , instrument (String) , ion source (String) , mass analyzer (String) , MS Assay Name (String) *, Raw Spectral Data File (String) *, Data transformation protocol (String) , Derived Spectral Data File (String) , Metabolite Identification protocol (String) , Metabolite Assignment File (String)
Not specified
'Assay - Material' Sample Type linked to Assay 'Chromatography'.
Input (Extract Name) (Registered Sample List) *, Chromatography protocol (Registered SOP) , Chromatography Instrument (String) , Column model (String) , Column type (String) , Labeled Extract Name (String) *
Not specified
'Assay - Material' Sample Type linked to Assay 'Metabolites extraction'.
Input (Sample Name) (Registered Sample List) *, Extraction (Registered SOP) , Post extraction (String) , Derivatization (Controlled Vocabulary - deCYPher_metabolomics_derivatization) , Extract Name (String) *
Not specified
Input (Registered Sample List) *, Chromatography protocol (Registered SOP) , Chromatography Instrument (String) , Column model (String) , Column type (String) , Labeled Extract Name (String)
Genome assembly
Input (Registered Sample List) *, sequence assembly protocol (String) *, FASTA (String) *, FASTA URL (String) , ASSEMBLYNAME (String) *, ASSEMBLY_TYPE (Controlled Vocabulary - ENA ASSEMBLY_TYPE) *, COVERAGE (String) *, PROGRAM (String) *, PLATFORM (String) *, MOLECULETYPE (String)
Test for MARS
Input (Registered Sample List) *, Analysis Title (String) *, Analysis Alias (String) *, Description (String) *, Experiment Type (Controlled Vocabulary - EVA Experiment Type CV) *, Reference (String) *, Data file Name (String) *
Input (Registered Sample List) *, library construction (String) *, library_construction_protocol (String) , title (String) *, design_description (String) , library_name (String) *, library_source (Controlled Vocabulary - library_source) *, library_strategy (Controlled Vocabulary - library_strategy) *, library_selection (Controlled Vocabulary - library_selection) *, library_layout (Controlled Vocabulary - library_layout) *, insert_size (String) , platform (Controlled Vocabulary - platform) *, instrument_model (Controlled Vocabulary - instrument_model) *, accession (String) , submission_date (String) , status (Controlled Vocabulary - status)
