More information about DANIO-CODE can be found at the official homepage. For a full description of how to use the DCC see the wiki.
Example CSV Files
An excel document with an example upload can be found at this link.
In order to use this as a batch upload csv file the first column must be removed and this file must be saved
in any supported CSV format from excel.
You can find the an example of a correctly formated CSV file at this link. If you open this file in excel please reformat the sequencing__sequencing_date to the correct date format (YYYY-MM-DD).
A series corresponds to a research question/experiment, which motivates the generation of the data. It is thereby connecting biosamples with each other.
A title given to the series.
The Series Type is either Survey or Case Control. A survey is collection of samples without any further order to them, i.e. the samples were not ordered into cases. In Case Control, biosamples are ordered into cases, e.g. treatment and control.
The description of the series. This can entail the research question, the aim of the experiments, a description of the different cases in case control studies, etc.
The DOI of the published results of this series.
The ID to the uploaded Series in GEO or SRA.
If the series should be publicly available or only to members of DANIO-CODE
A biosample corresponds to the physical entity which is the source of the gene material. One biosample entity includes all its biological replicates.
The lab which handled the biosample and the extraction of the gene material.
The type describes the organic material of origin for the biosample.
The site or tissue type of the sample (controlled only required for sample type tissue).
The developmental stage of the organism (required for sample type whole organism and tissue).
The hours between fertilisation and the exitus of the organism or extrusion of the sample (only applicable for sample type whole organism and tissue).
The specific biological background of the biosample (controlled).
A description of the sample (optional).
The mutation of the biosample, i.e. the targeted Gene.
The origin/distributor of the specific fish strain (optional).
The treatment applied on the sample (optional).
The sex of the biosample (optional).
Cell line type
The type of the cell line (only applicable for the biosample type “cell line”).
The technique used to produce the sequenced library, e.g. RNA-seq, ChIP-seq (controlled)
The lab which applied the assay on the biosample
A more detailed description of the assay, e.g. the protocol.
The target-chemical of the different IP-seq assay (required for ChIP-seq, SELEX-seq, RIP-seq, PAR-Clip-seq,
iCLIP-seq, ChIP-exo-seq, Methyl-seq)
The library preparation used for RNA-based assays, e.g. poly(A)+, poly(A)-, rRNA depletion, etc. (required for RNA-seq, short-RNA-seq, miRNA-seq, Ribo-seq, RIP-seq,
PAR-Clip-seq, iCLIP-seq, GRO-seq, CAGE-seq)
The applied assay which will be sequenced and which is the product of an assay applied to a biosample entity, i.e. the group of replicates.
The specific sequencing techniques used to produce the data sets.
The sequencing platform used to produce the data (controlled).
The sequencing instrument used to produce the data (controlled).
The lab which performed the sequencing (controlled).
The direction the reads have, with respect to the target mRNA (required for RNA based assays, controlled)
The date the sequencing was performed in the ISO 8601, i.e. YYYY-MM-DD. If the exact date is unknown, enter at least the year and 01 for the month or day, respectively.
The specific chemistry version used for the sequencing (optional).
Maximum read length
The longest read length of the sequencing (optional).
The sequencing direction mode, i.e.single/paired ended (controlled)
The data which is the result of all the steps above.
The name of the sequencing file, if it is inside a folder this field should contain the file path from the user directory (only one filename per sequencing for single ended and two for paired end sequenced files)