- \n
- microarray analysis<\/li>\n
- RNA Seq analysis– RNASeq data contains information about both nucleotide sequence and gene expression.<\/li>\n<\/ul>\n
Recommendations<\/h2>\n
Summary<\/span><\/h3>\n
- \n
- We recommend the existing format standards laid out by the repositories such as NCBI (GEO) \u00a0and EBI Array Express + \u00a0ENA<\/span><\/li>\n
- We recommend using ontologies and controlled vocabularies to annotate the required metadata.<\/span><\/li>\n<\/ol>\n
\nData formats<\/h3>\n
For microarray analysis:<\/h3>\n
- \n
- We recommend the existing format standards laid out by the repositories such as NCBI (GEO) \u00a0and EBI Array Express + \u00a0ENA<\/li>\n<\/ul>\n<\/div>\n
For RNA Seq analysis:<\/h3>\n
The NCBI SRA database (http:\/\/www.ncbi.nlm.nih.gov\/Traces\/sra\/<\/a>) is the official repository for the actual sequence data, produced in the form of FASTQ and\/or BAM files.<\/p>\n
For more information on formats:<\/p>\n
- \n
- FASTQ<\/a>: https:\/\/en.wikipedia.org\/wiki\/FASTQ_format<\/a><\/li>\n
- BAM<\/a> files: https:\/\/www.broadinstitute.org\/igv\/BAM<\/a><\/li>\n<\/ul>\n
Convert data format<\/strong>
\nYou can convert different formats to FASTQ or BAM using the Bioconvert tool<\/a>.<\/p>\n![\"https:\/\/bioconvert.readthedocs.io\/en\/master\/_images\/conversion.png\"](\"https:\/\/bioconvert.readthedocs.io\/en\/master\/_images\/conversion.png\")
<\/p>\n<\/p>\n
Metadata<\/h3>\n
Metadata is important for all gene expression studies – whether\u00a0 microarray or RNA Seq data.<\/p>\n
- \n
- Microarray data: NCBI-GEO- MIAMI compliant- http:\/\/www.ncbi.nlm.nih.gov\/geo\/info\/MIAME.htm<\/a><\/li>\n
- RNA-Seq data – follow the guidelines for MIAME as far as applicable (FastQ)<\/li>\n<\/ul>\n
For BAM files – additional info needed:<\/p>\n
- \n
- mapping software<\/li>\n
- mismatch settings<\/li>\n
- reference sequences used such as IWGSC survey sequences or MIPS gene models, or transcriptome assembly<\/li>\n<\/ul>\n
Please refer to this paper for more information:<\/p>\n
https:\/\/www.betacell.org\/documents\/administered\/about\/guidelines\/ENCODE_BCBC_RNA-Seq_Standards_V01_20110503.pdf<\/a><\/p>\n
Vocabularies<\/h3>\n
We recommend using ontologies and controlled vocabularies to annotate the required metadata. Please see the recommendations on the detailed page: Ontologies and Vocabularies<\/a><\/p>\n
- \n
- Plant Ontology terms to describe the plant tissues and developmental stage<\/li>\n
- Plant Environment Ontology\u00a0 to describe the experimental conditions<\/li>\n
- Plant Stress Ontology to describe the treatments with pathogens, stress conditions (proposed)<\/li>\n
- Gene Ontology is the standard for the functional analysis<\/li>\n
- Microarray ontology (MO) terms mapped to the OBI\/OBO foundry ontology terms – MGED ontology (http:\/\/bioportal.bioontology.org\/ontologies\/MO?p=classes<\/a>)<\/li>\n<\/ul>\n
<\/p>\n
<\/p>\n
Written on:<\/span>\u00a0WDI working group
\nPublished on:<\/span>\u00a0 02 October 2014
\nUpdated on:<\/span> 27 April 2015<\/div>\n<\/p>\n","protected":false},"excerpt":{"rendered":"
Gene expression analysis measures the abundance of the mRNA molecules, and gives us insight into the regulation of the genes of interest.\u00a0Machinery in the cell reads the sequence of the gene in groups of three bases. Each group of three bases (codon) corresponds to one of 20 different amino acids used to build a protein.” […]<\/p>\n","protected":false},"author":11,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"open","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-35","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages\/35","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/comments?post=35"}],"version-history":[{"count":0,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages\/35\/revisions"}],"wp:attachment":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/media?parent=35"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
- RNA-Seq data – follow the guidelines for MIAME as far as applicable (FastQ)<\/li>\n<\/ul>\n
- BAM<\/a> files: https:\/\/www.broadinstitute.org\/igv\/BAM<\/a><\/li>\n<\/ul>\n
- FASTQ<\/a>: https:\/\/en.wikipedia.org\/wiki\/FASTQ_format<\/a><\/li>\n
- We recommend using ontologies and controlled vocabularies to annotate the required metadata.<\/span><\/li>\n<\/ol>\n
- We recommend the existing format standards laid out by the repositories such as NCBI (GEO) \u00a0and EBI Array Express + \u00a0ENA<\/span><\/li>\n