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).

Terms

Series

A series corresponds to a research question/experiment, which motivates the generation of the data. It is thereby connecting biosamples with each other.
Title
A title given to the series.
Series Type
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.
Description
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.
Reference
The DOI of the published results of this series.
GEO/SRA ID
The ID to the uploaded Series in GEO or SRA.
Public
If the series should be publicly available or only to members of DANIO-CODE

Biosample

A biosample corresponds to the physical entity which is the source of the gene material. One biosample entity includes all its biological replicates.
Lab
The lab which handled the biosample and the extraction of the gene material.
Sample Type
The type describes the organic material of origin for the biosample.
Anatomical Term
The site or tissue type of the sample (controlled only required for sample type tissue).
Stage
The developmental stage of the organism (required for sample type whole organism and tissue).
Post Fertilization
The hours between fertilisation and the exitus of the organism or extrusion of the sample (only applicable for sample type whole organism and tissue).
Genetic Background
The specific biological background of the biosample (controlled).
Description
A description of the sample (optional).
Mutation description
The mutation of the biosample, i.e. the targeted Gene.
Source
The origin/distributor of the specific fish strain (optional).
Treatment
The treatment applied on the sample (optional).
Sex
The sex of the biosample (optional).
Cell line type
The type of the cell line (only applicable for the biosample type “cell line”).

Assay

Assay Type
The technique used to produce the sequenced library, e.g. RNA-seq, ChIP-seq (controlled)
Lab
The lab which applied the assay on the biosample
Description
A more detailed description of the assay, e.g. the protocol.
Target
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)
Library Preparation
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)

Applied assay

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.

Sequencing

The specific sequencing techniques used to produce the data sets.
Platform
The sequencing platform used to produce the data (controlled).
Instrument
The sequencing instrument used to produce the data (controlled).
Lab
The lab which performed the sequencing (controlled).
Strand Mode
The direction the reads have, with respect to the target mRNA (required for RNA based assays, controlled)
Sequencing Date
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.
Chemistry Version
The specific chemistry version used for the sequencing (optional).
Maximum read length
The longest read length of the sequencing (optional).
Sequencing mode
The sequencing direction mode, i.e.single/paired ended (controlled)

Data

The data which is the result of all the steps above.
File
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)

Video Tutorial

Name
initial entry
complete upload
with associated files
Name
whole organism
tissue
stem cells
cell line
Name
abdominal musculature
abducens motor nucleus
abductor hyohyoid
abductor muscle
abductor profundus
absorptive cell
accessory chamber of the maxillary blood sinus
accessory pretectal nucleus
acellular anatomical structure
acid secreting cell
acinar cell
actinotrichium
adaxial cell
adductor
adductor arcus palatini
adductor hyohyoid
adductor hyomandibulae
adductor mandibulae
adductor mandibulae complex
adductor muscle
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Lab Name Principal Investigator Institution Country
Daub Lab Carsten Daub KI Sweden
Wardle Lab Fiona Wardle King's College London England
Mueller lab Ferenc Mueller University of Birmingham UK
Shkumatava Lab Alena Shkumatava Institut Curie France
Sauka-Spengler Lab Tatjana Sauka-Spengler University of Oxford UK
Giraldez Lab Antonio Giraldez Yale USA
Winata Lab Cecilia Winata IIMCB Warsaw Poland
Mathavan Lab Sinnakaruppan Mathavan NTU Medical School Singapore
Onichtchouk Lab Daria Onichtchouk University of Freiburg Germany
Busch-Nentwich Lab Elisabeth Busch-Nentwich Wellcome Trust Sanger Institute UK
Lenhard Lab Boris Lenhard Imperial College London UK
Zon Lab Leonard Zon Boston Children's Hospital USA
Chatterjee Lab Aniruddha Chatterjee Dunedin School of Medicine; University of Otago New Zealand
MRC-CSC Genomics facility MRC-CSC UK
Barts and The London Genome Center Queen Mary University of London UK
Rotterdam Genomics core Erasmus MC Nederland
Vaquerizas Lab Juan M. Vaquerizas Max Planck Institute for Molecular Biomedicine Germany
Driever Lab Wolfgang Driever University of Freiburg Germany
Strahle Lab Uwe Strähle Karlsruhe Institute of Technology Germany
RIKEN Piero Carninci RIKEN Japan
Name
RNA-seq
short-RNA-seq
ChIP-seq
DNAse-seq
Hi-C-seq
ChIA-PET-seq
FAIRE-seq
ATAC-seq
CAGE-seq
Bru-seq
PAS-seq
Ribo-seq
SELEX-seq
STARR-seq
Capture-C-seq
RIP-seq
PAR-Clip-seq
iCLIP-seq
ChIP-exo-seq
BS-seq
Name
1-cell
2-cell
4-cell
8-cell
16-cell
32-cell
64-cell
128-cell
256-cell
512-cell
1k-cell
High
Oblong
Sphere
Dome
30%-epiboly
50%-epiboly
Germ-ring
Shield
75%-epiboly
Name
AB
AB/C32
AB/EKW
AB/TL
AB/TU
C32
KOLN
DAR
EKW
HK/AB
HK/SING
HK
IND
INDO
SPF 5-D
SPF AB
NA
RW
SAT
SING
Name
AB SOLiD System
ABI 377 automated sequencer
Genome Sequence 20
Genome Sequence FLX+ / FLX
HiSeq X Ten
HiSeq 2000
HiSeq 2500
HiSeq 3000
HiSeq 4000
HiSeq 5000
NextSeq 500 High-Output
NextSeq 500 Mid-Output
HiSeq High-Output v4
HiSeq High-Output v3
HiSeq Rapid Run
HiScanSQ
GAIIx
Li-Cor 4300 DNA Analysis System
MiSeq v3
HiSeq 1500
Name
Illumina
Ion
PacBio
Roche 454
SOLiD
Name
m
f
Name
unstranded
forward
reverse