Automated RNA Access Installation Guide

For Agilent NGS Workstation Option B

Description
Requirements
Installation
Protocol
License

Description

This document describes how to set up the automated RNA Access protocol for the Agilent NGS Workstation created at NGI Stockholm.

Requirements

Item	Note
Agilent NGS Workstation	⚠️ Option B configuration only
Eppendorf twin.tec 96 PCR plate	Eppendorf, cat# 0030 128.672 (int); 951020460 (US)
Nunc deepwell 1.3 mL plate	Thermo Scientific, cat# 260251
ABgene 2.2 mL storage plate Mk.II	Thermo Scientific, cat# AB-0933

Labware definitions | Provided in all_labware_liquids.vzp Liquid classes definition | Provided in all_labware_liquids.vzp

* provided in all_labware_liquids.vzp

Included files

illumina_spri.pro
rna-access.js
rna-access.rst
rna-access.VWForm
rna-access_atailing-ligation_setup.pro
rna-access_capture.rst
rna-access_cdna-spri_setup.pro
rna-access_elution.pro
rna-access_filler.pro
rna-access_hyb.pro
rna-access_ligation-spri_setup.pro
rna-access_ligation.pro
rna-access_pcr.pro
rna-access_reaction.pro
rna-access_spri-atailing_setup.pro
rna-access_spri-pcr_setup.pro
rna-access_spri_setup.pro
rna-access_wash.pro
all_labware_liquids.vzp
resources/1313497192_media_controls_light_pause.png
resources/1313497517_media_controls_light_play.png
resources/clear_inventory.bat
resources/clear_inventory.sql

Installation

Download files

Using Git

Clone into https://github.com/ngi-automation/rna-access.git from the Protocol Files directory:

cd "C:\VWorks Workspace\Protocol Files"
git clone https://github.com/ngi-automation/rna-access.git

Alternatively, download the compressed folder from: https://github.com/ngi-automation/rna-access/archive/master.zip and extract to C:\VWorks Workspace\Protocol Files. Rename the resulting rna-access-master folder to rna-access. The path to the folder containing the extracted files should then be C:\VWorks Workspace\Protocol Files\rna-access.

Configure

Labware and and liquid class definitions

Use the import feature in VWorks from File › Importin the toolbar and select the all_labware_liquids.vzp file included. See the VWorks Knowledge Base for more information.

Device files

Device files and profiles are system specific and will not be provided. Two different Bravo configurations are used in the RNA Access protocols (one being the "standard" configuration):

Standard configuration

Position	Type	Part#
1–3, 8	Deck Platepad	`G5498b#004`
4, 6	Peltier Thermal Station (Inheco)	`G5498b#021`
5	Orbital Shaking Station	`G5498b#033`
7	Magnetic Bead Accessory	`G5498b#008`
9	Thermal Station (ThermoCube)	`G5498b#036`/`7`/`8`

Capture configuration

Same as above but with the following modification:

Position	Type	Part#
6	Thermal Station w Deepwell Plate Insert	`G5498b#012`

For reference see Agilent's accessories catalog for the Bravo.

Each .pro file must have the correct device file set:

Protocol file	Device file
`rna-access_reaction.pro`	Standard
`rna-access_pcr.pro`	Standard
`illumina_spri.pro`	Standard
`rna-access_hyb.pro`	Standard
`rna-access_filler.pro`	Standard
`rna-access_wash.pro`	Capture
`rna-access_elution.pro`	Capture
`rna-access_atailing-ligation_setup.pro`	Standard
`rna-access_cdna-spri_setup.pro`	Standard
`rna-access_ligation-spri_setup.pro`	Standard
`rna-access_spri-pcr_setup.pro`	Standard
`rna-access_spri-atailing_setup.pro`	Standard
`rna-access_spri_setup.pro`	Standard

See the VWorks Knowledge Base for more information on how to select the device file.

Protocol

See the NGI Stockholm/SciLifeLab Standard Operating Procedure (work in progress).

License

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

The full license can also be found in the file LICENSE and must included when redistributing the software.

If this method is used to generate results for publication we ask that you include a reference to this repository, something like:

Automation protocols made available by the National Genomics Infrastructure Stockholm at https://github.com/ngi-automation/rna-access

VWorks Automation Control, Bravo and other things relating to the Agilent NGS Workstation are trademarks owned by Agilent Technologies, Inc. (Santa Clara, CA 95052-8058, US).

RNA Access is a trademark owned by Illumina, Inc. (San Diego, CA 92122 US)

National Genomics Infrastructure at SciLifeLab
joel.gruselius@scilifelab.se
April 2016

ngi-automation/rna-access