For Agilent NGS Workstation Option B
This document describes how to set up NGI Stockholms TruSeq Stranded mRNA method for the Agilent NGS Workstation. This protocol is used to prepare up to 96 samples with Illumina’s TruSeq Stranded mRNA kit.
- Agilent NGS Workstation
⚠️ Option B only - Consumables
- 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*
- Liquid classes definition*
* provided in all_labware_liquids.vzp
truseq_rna.VWForm
rna_prep_v1203.pro
truseq_stranded_runset.rst
truseq_stranded_adenylation.pro
truseq_stranded_ligation.pro
truseq_startup.pro
truseq_startup_v1201.js
truseq_stranded_ligation.VWForm
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
Clone into https://github.com/ngi-automation/truseq-stranded-mrna.git from the Protocol Files directory:
cd "C:\VWorks Workspace\Protocol Files"
git clone https://github.com/ngi-automation/truseq-stranded-mrna.gitAlternatively, download the compressed folder from:
https://github.com/ngi-automation/truseq-stranded-mrna/archive/master.zip
and extract to C:\VWorks Workspace\Protocol Files. Rename the resulting truseq-stranded-mrna-master folder to truseq-stranded-mrna. The path to the folder containing the extracted files should then be C:\VWorks Workspace\Protocol Files\truseq-stranded-mrna.
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 and profiles are system specific and will not be provided. The "standard" Bravo configuration is used in the TruSeq RNA protocols:
| 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 |
.pro file must have the correct device file set.
See the VWorks Knowledge Base for more information on how to select the device file.
Link to PDF with instructions.
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 NGI Sweden at https://github.com/ngi-automation/truseq-stranded-mrna
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).
TruSeq and TruSeq Stranded mRNA are trademarks owned by Illumina, Inc. (San Diego, CA 92122 US).
National Genomics Infrastructure at SciLifeLab
joel.gruselius@scilifelab.se
July 2014