TruSeq Small RNA v1.0

Overview

TruSeq Small RNA v1.0 includes the following functionality:

• Preconfigured TruSeq Small RNA v1.0 protocol that explains how to prepare total RNA or purified small RNA using a Illumina® TruSeq® Small RNA Library Prep Kit.

• Automated calculation of sample and buffer volumes.

• Automated calculation or display of reagents at every step in the protocol.

• Automatic step transition when required.

• Automatic placement of samples when necessary.

• Automated assignment of QC Pass/Fail, based on user-selected threshold values.

• A routing script that allows sequencing of libraries using any Illumina sequencing instrument.

It is not required to have the total RNA samples quantified prior to starting this protocol, however it is highly recommended to ensure the starting number of samples.

Protocol 1: TruSeq Small RNA v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Ligate Adapters (TruSeq Small RNA v1.0)

• Master Step Name = Ligate Adapters (TruSeq Small RNA v1.0.10)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

• Reagent Kits

  • T4 RNA Ligase 2, Deletion Mutant

    • Supplier = Epicentre

    • Catalog Number = LR2D1132K; LR2D11310K

  • TruSeq Small RNA Library Prep Kit, Core Solutions

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

  • TruSeq Small RNA Library Prep Kit, Indices A, B, C or D

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

• Control Types

  • Human Brain Total RNA

    • Supplier = Thermo Fisher Scientific

    • Catalog Number = AM7962

Automations

bash -l -c " /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} &&  /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::HML Volume (ul):: = step.::Total samples:: * 2.2) ; (step.::RNase Inhibitor Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::T4 RNA Ligase 2, Depletion Mutant Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::RA5 Volume (ul):: = step.::Total samples:: * 1.21) ; (step.::10mM ATP Volume (ul):: = step.::Total samples:: * 1.21) ; (step.::T4 RNA Ligase Volume (ul):: = step.::Total samples:: * 1.21)' -log {compoundOutputFileLuid1}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table

  • Column Headers

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    Well