HiScanSQ System Site Preparation Guide

Transcription

1 HiScanSQ System Site Preparation Guide FOR RESEARCH USE ONLY Introduction 3 Supported Configurations 4 User-Supplied Equipment and Materials 5 Delivery and Installation 6 Operation, Maintenance, and Service 7 Laboratory Requirements 7 Environmental Constraints 12 Workstation, Network, and Data Storage 13 Data Processing and Analysis 13 Technical Assistance 15 ILLUMINA PROPRIETARY Catalog # SY Part # Rev. D October 2010

2 This document and its contents are proprietary to Illumina, Inc. and its affiliates ("Illumina"), and are intended solely for the contractual use of its customer in connection with the use of the product(s) described herein and for no other purpose. This document and its contents shall not be used or distributed for any other purpose and/or otherwise communicated, disclosed, or reproduced in any way whatsoever without the prior written consent of Illumina. Illumina does not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any third parties by this document. The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in order to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must be fully read and understood prior to using such product(s). FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN MAY RESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS, AND DAMAGE TO OTHER PROPERTY. ILLUMINA DOES NOT ASSUME ANY LIABILITY ARISING OUT OF THE IMPROPER USE OF THE PRODUCT(S) DESCRIBED HEREIN (INCLUDING PARTS THEREOF OR SOFTWARE) OR ANY USE OF SUCH PRODUCT(S) OUTSIDE THE SCOPE OF THE EXPRESS WRITTEN LICENSES OR PERMISSIONS GRANTED BY ILLUMINA IN CONNECTION WITH CUSTOMER'S ACQUISITION OF SUCH PRODUCT(S). FOR RESEARCH USE ONLY 2010 Illumina, Inc. All rights reserved. Illumina, illuminadx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iselect, CSPro, GenomeStudio, Genetic Energy, HiSeq, HiScan, Eco, and TruSeq are registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.

3 Introduction Thank you for purchasing your Illumina system. Figure 1 HiScanSQ System Introduction This manual provides the laboratory space requirements, electrical requirements, environmental constraints, and computing requirements for the following Illumina products included in the HiScan TM SQ System: HiScan TM Reader SQ Module NOTE If your system does not include the SQ Module, specifications and requirements outlined in this document for the SQ Module do not apply to your lab setup. Dedicated Computer Workstation HiScanSQ System Site Preparation Guide 3

4 Supported Configurations The HiScanSQ System can be installed with or without the AutoLoader 2.x to automate BeadChip loading. The following configurations are supported: Without AutoLoader 2.x HiScan Reader by itself HiScan Reader with the SQ Module In both of these configurations, both the HiScan Reader and the SQ Module face forward on the lab bench. The SQ Module must be installed on the right side of the HiScan Reader. (See Figure 1.) With AutoLoader 2.x Single-reader configurations: One HiScan Reader with the AutoLoader 2.x One HiScan Reader with the SQ Module and AutoLoader 2.x In both of these configurations, the HiScan Reader is turned sideways on the lab bench so its tray is facing the AutoLoader 2.x on the left. If the SQ Module is installed, it must be facing forward on the right side of the HiScan Reader. Figure 2 Single-Reader Configuration with the HiScan Reader, SQ Module, and AutoLoader 2.x Dual-reader configurations: One iscan and one HiScan Reader with the AutoLoader 2.x One iscan, one HiScan Reader, and one SQ Module with the AutoLoader 2.x Two HiScan Readers with the AutoLoader 2.x Two HiScan Readers and one SQ Module with the AutoLoader 2.x In a dual-reader configuration, both readers are turned sideways with their trays facing the AutoLoader 2.x between them. If your system includes one iscan and one HiScan Reader, the HiScan Reader must be installed on the right side of the AutoLoader 2.x, with its tray facing left. A dual-reader configuration can only be used with one SQ Module installed. The SQ Module must be installed facing forward on the right side of the right HiScan Reader in the configuration. 4 Part # Rev. D

5 Figure 3 Dual-Reader Configuration with an iscan, HiScan Reader, SQ Module, and AutoLoader 2.x User-Supplied Equipment and Materials Equipment Required Obtain the equipment listed in this table prior to using the HiScanSQ System. Table 1 User-Supplied Equipment Required Item Balance, top-loading, digital, 420 g capacity Source Sartorius, Model CPA423S (or similar) User-Supplied Equipment and Materials Bottle rack, 6-position 250 ml centrifuge tube, epoxy-coated cbot Cluster Generation System Note: The cbot Cluster Generation System is required only if your system includes the SQ Module for sequencing. If you did not purchase the optional SQ Module, you do not need the cbot. Freezer, 20º C Ice bucket Refrigerator, 4º C Tweezers, square-tip plastic LabScientific, catalog # CBR 200 Illumina, catalog # SY General lab supplier General lab supplier General lab supplier McMaster-Carr, catalog # 7003A22 (or similar) Materials Required Obtain the materials listed in this table prior to using the HiScanSQ System. Table 2 User-Supplied Materials Required Item Source Alcohol prep pads, 70% isopropyl VWR, catalog # HiScanSQ System Site Preparation Guide 5

6 Table 2 User-Supplied Materials Required Item Ethanol, 99.5%, ACS, absolute (optional) Gloves, powder-free disposable, latex or nitrile Source Fisher Scientific, catalog # AC General lab supplier Lens cleaning tissues, 4 x 6 inches VWR, catalog # Pipette tips, 200 µl Pipette tips, 1000 µl Tubes, 15 ml polypropylene conical centrifuge with cap Tubes, 50 ml polypropylene conical centrifuge with cap Tubes, 250 ml polypropylene conical centrifuge with cap General lab supplier General lab supplier Corning, catalog # Corning, catalog # Corning, catalog # Syringes, Luer-Lok 10 ml BD, catalog # Water, 18 MOhm Millipore Wiper, delicate task, low-lint VWR, catalog # Delivery and Installation The lab space and bench must be ready in advance of delivery. For more information, see Laboratory Requirements on page 7. Only Illumina-authorized personnel should unload and install the HiScanSQ System. The instruments are heavy and could cause serious injury if dropped or mishandled. In addition, the instruments could be damaged or broken. For more information, refer to the HiScanSQ System Safety and Compliance Booklet. 6 Part # Rev. D

7 Operation, Maintenance, and Service Operating Instructions Operating instructions for this system are included in the HiScanSQ System User Guide. Maintenance Maintenance procedures that users are expected to perform are included in the HiScanSQ System User Guide. Service This system contains no user-serviceable components. Contact Illumina Customer Support to schedule a service call if necessary (see Technical Assistance on page 15). Laboratory Requirements Lab Space and Bench The HiScanSQ System is shipped in four crates. Refer to Crate Dimensions and Contents on page 9 to determine the minimum door width required to accommodate the shipping crates. Operation, Maintenance, and Service Lab Space Requirements Reserve sufficient lab space and a bench that is capable of safely supporting the HiScanSQ System and its dedicated computer workstation. The components of the HiScanSQ System must be located so users can quickly disconnect the power cord from the outlet. The HiScan Reader and the SQ Module must be placed on the bench at the same elevation. There must be 120 cm (47.3 inches) of vertical clearance above the bench to allow room for service. Make sure that the HiScanSQ System is accessible from all sides. Lab Bench Guidelines Because the HiScanSQ System must be accessible from all sides, Illumina strongly recommends placing the system on a mobile lab bench with locking wheels (casters). The bench should include a lower shelf to hold the computer workstation and UPS. The lower shelf must have 58.4 cm (23 inches) of vertical clearance and be capable of supporting up to 97.5 kg (215 lbs). The bench top must be capable of supporting the weight of the remaining components of your system. Depending on which components will be installed, the bench must meet the following guidelines. HiScanSQ System Site Preparation Guide 7

8 Table 3 Laboratory Bench Guidelines Components Width Height Depth Weight Capacity Locking Casters HiScan Reader cm (60 inches) 76.2 to 91.4 cm (30 to 36 inches) 91.4 cm (36 inches) kg (300 lbs) Yes HiScan Reader, AutoLoader 2.x cm (84 inches) for a single-reader configuration cm (120 inches) for a dual-reader configuration 76.2 to 91.4 cm (30 to 36 inches) 91.4 cm (36 inches) kg (610 lbs) for a single-reader configuration 440 kg (970 lbs) for a dual-reader configuration Yes HiScan Reader, SQ Module cm (72 inches) 76.2 to 91.4 cm (30 to 36 inches) 91.4 cm (36 inches) kg (500 lbs) Yes HiScan Reader, SQ Module, AutoLoader 2.x cm (96 inches) for a single-reader configuration cm (120 inches) for a dual-reader configuration 76.2 to 91.4 cm (30 to 36 inches) 91.4 cm (36 inches) kg (810 lbs) for a single-reader configuration kg (1170 lbs) for a dual-reader configuration Yes For North American customers, Illumina recommends the following mobile lab benches from Bench-Craft ( HiScan Reader: HS S-P2 with casters HiScan Reader and AutoLoader 2.x: Single-reader configuration: HS S-P2 with casters Dual-reader configuration: HS S-P2 with casters HiScan Reader and SQ Module: HS S-P2 with casters HiScan Reader, SQ Module, and AutoLoader 2.x: Single-reader configuration: HS S-P2 with casters Dual-reader configuration: HS S-P2 with casters NOTE The S in the bench name indicates that there is a lower shelf. The P2 in the name indicates that there are two outlets on the rear of the bench. 8 Part # Rev. D

9 Crate Dimensions and Contents The components of the HiScanSQ System are shipped in four crates with the following dimensions and contents: Table 4 Container Dimensions and Contents Crate Contents Width Height Depth Weight HiScan Reader SQ Module Uninterruptible Power Supply (National, International, or Japan) Shipped in a box on a pallet. Workstation PC Monitor Waste bottle Reagent racks Instrument Panels Power Cord(s): One domestic power cord (U.S.), or Three international power cords (UK, EU, China) cm (44 inches) 81.3 cm (32 inches) 77.5 cm (30.5 inches) 104 cm (41 inches) cm (45 inches) 81.3 cm (32 inches) cm (43 inches) kg (525 lbs) 94 cm (37 inches) kg (353 lbs) 51 cm (20 inches) 61 cm (24 inches) 8.3 kg (177 lbs) 99.1 cm (39 inches) 81.3 cm (32 inches) 125 kg (275 lbs) Laboratory Requirements HiScanSQ System Dimensions and Weights The components of the HiScanSQ System have the following dimensions when installed. Figure 4 HiScanSQ System Dimensions and Bench Layout Depth = 69.8 cm (27.5 inches) Depth = 59 cm (23.2 inches) 74.5 cm (29.3 inches) 72.6 cm (28.6 inches) 71.7 cm (28.3 inches) 58.7 cm (23.1 inches) 5.1 cm (2 inches) HiScanSQ System Site Preparation Guide 9

10 NOTE For dimensions and weight when the system includes the AutoLoader 2.x, refer to the AutoLoader 2.x User Guide. Table 5 HiScanSQ System Dimensions and Weight System Component Width Height Depth Weight HiScan Reader 71.7 cm (28.3 inches) Note: Allow 7.6 cm (3 inches) of clearance on the left side for cables 74.5 cm (29.3 inches) 69.8 cm (27.5 inches) kg (300 lbs) SQ Module 58.7 cm (23.1 inches) Note: Allow 7.6 cm (3 inches) of clearance on the right side for cables 72.6 cm (28.6 inches) 59 cm (23.2 inches) 88 kg (194 lbs) Computer Workstation 21.6 cm (8.5 inches) 57 cm (22.3 inches) 55.4 cm (21.8 inches) 34 kg (75 lbs) For normal operation, place the HiScan Reader and SQ Module 5.1 cm (2 inches) apart on the bench, with the SQ Module on the right side, as shown in Figure 4. To allow for service to the instruments, the instruments in the HiScanSQ System must be accessible from all sides. Additionally, there needs to be: Space on the bench to separate the instruments by 30.4 cm (12 inches) 45.5 cm (18 inches) of clearance above the HiScan Reader 50.8 cm (20 inches) of clearance on the left side of the HiScan Reader and on the right side of the SQ Module Electrical Requirements The power consumption of the HiScanSQ System, including all its components, is described in this section. HiScan Reader VAC 50/60 Hz 650 W Fuse: T10A, 250VAC (Slo Blow) SQ Module VAC 50/60 Hz 500 W Fuse: T6.3A, 250VAC (Slo Blow) 10 Part # Rev. D

11 Table 6 HiScanSQ System Electrical Requirements Equipment HiScanSQ System Description The building should be wired with the following receptacles: volts AC: A 20-amp grounded, dedicated line with proper voltage and electrical ground is required. Depending on your region, wire your lab for the one of the following receptacles: North America: NEMA 5-20R (Interpower Corp., part # or equivalent) Japan: NEMA L5-30R Laboratory Requirements volts AC: A 10-amp grounded line with proper voltage and electrical ground is required. Power Line Regulator Uninterruptible Power Supply If the voltage fluctuates more than 10%, a power line regulator is required. See Table 7 on page 11 (shipped with the instrument). Table 7 HiScanSQ System Uninterruptible Power Supply (UPS) APC Smart- UPS Model Max Watts Max Current Input Voltage (Nominal) Input Connection Typical UPS Runtime at 50% Load Typical UPS Runtime at 100% Load SUA2200XL 1980 W 2200 VA 120V NEMA 5-20P 28.5 min min. SUA2200JB 1980 W 2200 VA 100V NEMA L5-30P 28.5 min min. SUA2200XLI 1980 W 2200 VA 230V IEC-320 C20 Schuko CEE 7/EU1-16P British BS1363A 28.5 min min. Electrical Standards The HiScanSQ System is certified to the following standards: UL STD CSA STD C22.2 No Laser Safety IEC Low Voltage Directive (Product Safety) IEC EMC Directive IEC HiScanSQ System Site Preparation Guide 11

12 Power Supply The HiScanSQ System comes with an international standard IEC C13 receptacle and is shipped with a region-specific power cord and a region-specific uninterruptible power supply (UPS). Never use an extension cord to connect the HiScanSQ System and its components. To obtain equivalent receptacles, power cords, or UPSs that comply with local standards for facilities outside the referenced regions, consult a third-party supplier such as Interpower Corporation ( Environmental Constraints Temperature and Humidity The lab should maintain a temperature between 22º C ± 3º C with the relative non-condensing humidity kept between 20 80%. Altitude Limitations Locate the system at an altitude of less than 2000 m (6500 feet). Air Quality The instruments are designed to be operated in a Pollution Degree II environment or better. A Pollution Degree II environment is defined as one which normally includes only nonconductive pollutants. Ventilation Heat output for the HiScanSQ System, including the monitor and PC, is a maximum 4000 BTU/h. Consult your facilities department regarding ventilation requirements for the level of heat output in your laboratory. 12 Part # Rev. D

13 Workstation, Network, and Data Storage Dedicated Workstation The HiScanSQ is shipped with a dedicated workstation that is customized to the latest system requirements. Contact Technical Support if you want more information about the computer specifications. The computer workstation is a dedicated subsystem of the instrument, and is not intended for use nor supported as a general-purpose workstation. Loading and using third-party software may result in down time, loss of data, or invalid data. Anti-Virus Software Anti-virus software is not provided because customer preferences and network requirements differ widely. Illumina strongly recommends that you purchase and install the anti-virus software of your choice to protect the computer against viruses. To avoid losing data: Do not run anti-virus software while the HiScanSQ is in use. Configure the anti-virus software to not automatically reboot the computer upon update. Exclude the data drive and application directory from any real-time file system protection. Network Considerations Illumina does not provide installation or technical support for networking in the dedicated workstation. However, your own IT people are free to install and maintain a network connection on the workstation during or after installation. Workstation, Network, and Data Storage NOTE Network maintenance activities should be reviewed for potential compatibility risks in relation to the Illumina system. To support the volume of data coming from the HiScanSQ System, you need a highthroughput Ethernet connection (1 Gigabit minimum) or other data transfer mechanism. If multiple sequencing instruments all copy to the same server, the server drive may not be fast enough to handle all the traffic. Consider having the instruments copy to different servers. If multiple sequencing instruments share a connection to copy to their target servers, the connection may not be fast enough to handle all the traffic. Consider having the instruments use different routes. Data Processing and Analysis Illumina s CASAVA analysis software may run on any 64-bit Unix variant, if all of the prerequisites described in this section are met. However, Illumina does not support any platform other than Linux. If you do not have a high-performance computing (HPC) system suitable for your sequencing needs, or if you question the suitability of your existing system, Illumina offers an optimized data processing solution: IlluminaCompute. HiScanSQ System Site Preparation Guide 13

14 IlluminaCompute is a scalable computing architecture for human-scale genomic data processing and analysis. IlluminaCompute provides a complete genomic data processing solution comprising hardware, software, and support services that can be deployed with minimal time and with no pre-existing computer infrastructure. The table below describes the standard IlluminaCompute packages, which all come configured with Red Hat Linux. You may find the information in the table useful for estimating the scale of the computing solution you require. Contact Illumina or your sales representative for more information. Table 8 IlluminaCompute HPC Systems NOTE If your HiScanSQ System includes two HiScan Readers, each with an SQ Module attached to enable sequencing, then the low-throughput configuration described below is enough for your needs. However, the low-throughput configuration is not scalable. If you intend to run more than two HiScanSQs, you should consider the medium- or highthroughput configurations. Product Low-Throughput Configuration Processes up to 200 gigabases/week (Not scalable) Medium-Throughput Configuration Processes up to 200 gigabases/week Medium-Throughput Upgrade Processes an additional 100 gigabases/week High-Throughput Configuration Processes up to 700 gigabases/week High-Throughput Upgrade Processes an additional 350 gigabases/week Optional Archive System Quantity and Description 1 Dell PowerEdge 900 series server: 16 CPU cores, 4 GB RAM each 1 Storage Shelf MD1200 series: 10 TB usable space (12 drives of directly attached storage) 1 Custom 14U Rack 1 APC Smart UPS APC Netshelter: 40U rack with 1U KMM console 3 Dell R610 Server: 8 CPU cores, 48 GB RAM each 3 Isilon IQ12000x storage modules 1 Serial MGT Console 16 2 Cisco 3750e switches Dell R610 Server: 8 CPU cores, 48 GB RAM each Isilon IQ12000x storage modules 1 APC Netshelter: 40U rack with 1U KMM console 1 Dell M1000e Blade Chassis with 8 M610 server blades (8 CPU cores, 48 GB RAM each) 3 Isilon IQ36000x storage modules 1 Serial MGT Console 48 2 Cisco 3750e switches Dell M1000e Blade Chassis with 16 M610 server blades (8 CPU cores, 48 GB RAM each) Isilon IQ36000x storage modules Cisco 3750e switches LT04 Archiving System, 32 TB 14 Part # Rev. D

15 Technical Assistance For technical assistance, contact Illumina Customer Support. Table 9 Illumina General Contact Information Illumina Website techsupport@illumina.com Table 10 Illumina Customer Support Telephone Numbers Region Contact Number North America toll-free ILMN ( ) Technical Assistance United Kingdom toll-free Germany toll-free Netherlands toll-free France toll-free Other European time zones Other regions and locations ILMN ( ) MSDSs Material safety data sheets (MSDSs) are available on the Illumina website at Product Documentation If you require additional product documentation, you can obtain PDFs from the Illumina website. Go to When you click on a link, you will be asked to log in to icom. After you log in, you can view or save the PDF. To register for an icom account, please visit HiScanSQ System Site Preparation Guide 15

16 Illumina, Inc Towne Centre Drive San Diego, CA ILMN (4566) (outside North America)