README.md

CDDRC Docs - Data Access

CDDRC Project Creation

To create a new project go to RedCap CDDRC project creation page and fill out the form. The tables below provide details on each of the fields in the project creation form.

Projects

Field Label	Description	Becomes Mosaic Project Attribute	Required
Project Name	Key term[s] to describe your project.		Yes
Project Description	Long form description used to record and note all necessary and desired aspects of your project.		Yes
Set project privacy level to protected.	Set to True if you do not want your project publicly accessible.		No (default: False)
Lab	Governing lab PI.	Yes	Yes
Institution	Lab and projects originating from this institution.	Yes	Yes
Organism	Organism under study. See 'Organism Table' below.	Yes	Yes
Organism Name	If the above option is 'Other', specify the organism here.		Yes*
Reference Genome	Organism reference genome See 'Reference Genome' Table below	Yes	Yes
Experiment Type	Experiment methodology See 'Experiment Type Table' below	Yes	Yes
Other Experiment Type	If the above option is 'Other', specify the type here.		Yes*
Experiment Platform	Platform used to generate experiment type. See 'Experiment Platform Table' below	Yes	Yes
Other Experiment Platform	If the above option is 'Other', specify the type here.		Yes*
Sequence Library Protocol Description	Allowed additional notes for sequence protocol.	Yes	No
Sequence Source	Where your project specific sequence was generated.	Yes	No
Genes of Interest	A comma separated list of specific genes of interest.	Gene Set	No
PCR Library Type	If any samples underwent PCR amplification	Yes	No (default: unknown)
Library Kit	Kits and reagents for sequencing methods.	Yes	No
Library Method	Library Method used in experiment.	Yes	No
Capture	Specific captured use in data generation.	Yes	No
Notes	Any additional project level notes.	Yes	No
Submitter First Name	First name of person submitting project request.	Yes	Yes
Submitter Last Name	Last name of person submitting project request.	Yes	Yes
Submitter Email	Email of person submitting project request.	Yes	Yes
Manifest	Downloadable Sample Manifest template See 'Manifest Fields Table' below		N/A
Manifest Upload	Upload section for completed above manifest.		Yes

Organism Selector

Organism
Alligator mississippiensis
Anolis carolinensis
Celegans elegans
Gallus gallus
Human
Mouse
Rat
Sheep
Xenopus tropicalis
Zebrafish
Other

Reference Genome Selector

Reference Genome	Description
GRCh37	Human build 37
GRCh38	Human build 38
GRCz11	Zebrafish build 11
GRCm39	Mouse build 39
unsupported	Other builds unsupported, contact us

Experiment Type Selector

Experiment Type	Description
CGH	Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells.
ChiP-on-chip	ChIP-on-chip is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray ("chip").
ChIP-Seq	ChIP-sequencing, is a method used to analyze protein interactions with DNA.
Directional mRNA Sequencing
DNA Methylation Analysis
Exon
Gene Expression
Genomic DNA Sequencing
Hi-C	Hi-C is a high-throughput genomic and epigenomic technique first described in 2009 by Lieberman-Aiden et al. to capture chromatin conformation.
HybMap
miRNA
Mononucleosome sequencing
Morpholino analysis
mRNA Sequencing
single cell RNA-seq
Small mRNA Sequencing
SNP
Targeted Genomic Resequencing
Transcriptome sequencing
Other

Experiment Platform Selector

Experiment Platform
Affymetrix Microarray
Agilent 1-color Microarray
Agilent 2-color Microarray
Functional Gene Analysis
Illumina HiSeq 4000 Sequencing
Ion Torrent
Life-SOLiD
Roche-454
Other

Manifest Fields

Currently available manifest fields.

Manifest Column Name	Becomes Mosaic Sample Attribute	Required
Sample ID	Yes	Yes
Individual ID	Yes	No
Internal ID	Yes	No
Stage	Yes	No
Treatment	Yes	No
Treatment Group	Yes	No
Gene Name	Yes	No
Ensembl ID	Yes	No
Molecule Type	Yes	No
Sample Volume	Yes	No
Organ	Yes	No
Tissue	Yes	No
Tissue Condition	Yes	No
Dose	Yes	No
Genotype/Genetic Modification	Yes	No
Phenotype	Yes	No
Expression Group	Yes	No
Analysis Group	Yes	No
Replica Number	Yes	No
Note	Yes	No