LibraryPreparation

Summary of SMaHT Portal object type LibraryPreparation . Its parent type is: Preparation. Types referencing this type are: Library. Property names in red are required properties; those in blue are identifying properties; and properties with types in green are reference properties.

Description: Library Preparation items contain more detailed information on library preparation protocols.

Tip

See actual LibraryPreparation data here

Required Properties

Property	Type	Description
submission_centers	SubmissionCenter array of string	See below for more details. See values here
submitted_id	string	See below for more details.

Identifying Properties

Property	Type	Description
accession	string	See below for more details.
submitted_id	string	See below for more details.
uuid	string	See below for more details.

Reference Properties

Property	Type	Description
consortia	Consortium array of string	See below for more details. See values here
preparation_kits	PreparationKit array of string	See below for more details.
submission_centers	SubmissionCenter array of string	See below for more details. See values here
treatments	Treatment array of string	See below for more details.

Properties

Property	Type	Description
accession	string	A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.]
adapter_inclusion_method  • Ligation  • Not Applicable  • Tagmentation	array of enum • min items: 1 • unique	Method of library preparation from an analyte.
alternate_accessions	array of string • restricted	Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.]
amplification_method  • MALBAC  • MDA  • Not Applicable  • PCR  • PTA	array of enum • min items: 1 • unique	Amplification method used to increase library products.
consortia	Consortium • array of string • unique	Consortia associated with this item. See values here
description	string	Plain text description of the item.
display_title	string • calculated	-
enzymes	array of string • min items: 1 • unique	Enzymes used in fragmentation. Required if fragmentation_method contains Restriction Enzyme or Transposase.
fragmentation_method  • Mechanical  • Not Applicable  • Restriction Enzyme  • Sonication  • Transposase	array of enum • min items: 1 • unique	Method used for nucleotide fragmentation.
insert_selection_method  • Affinity Enrichment  • Hybrid Selection  • Not applicable  • PCR  • PolyA Enrichment  • PolyT Enrichment  • rRNA Depletion	array of enum • min items: 1 • unique	Method for selecting inserts included in library.
preparation_kits	PreparationKit • array of string • min items: 1 • unique	Links to associated preparation kits.
rna_seq_protocol  • TruSeq  • Watchmaker	enum of string	Protocol used for RNA-seq assays.
size_selection_method  • Gel Electrophoresis  • Magnetic Beads  • Not Applicable	array of enum • min items: 1 • unique	Method for selecting fragment sizes.
status  • deleted  • draft  • in review ← default  • obsolete  • public  • released  • restricted	enum of string • default: in review	-
strand  • First Stranded  • Not Applicable  • Second Stranded  • Unstranded	enum of string	Library stranded-ness.
submission_centers	SubmissionCenter • array of string • unique	Submission Centers that created this item. See values here
submitted_id	string	Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_LIBRARY-PREPARATION_[A-Z0-9-_.]{4,}$
tags	array of string • min string length: 1 • max string length: 50 • unique • restricted	Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$
treatments	Treatment • array of string • min items: 1 • unique	Link to associated treatments performed during library preparation.
trim_adapter_sequence	boolean	Whether trimming adapter sequence is recommended.
uuid	string	Unique ID by which this object is identified.