Thermo Fisher Scientific GeneChip Data Collection User guide

For Research Use Only. Not for use in diagnostic procedures.

GeneChipTM Data Collection (GCDC)

USER GUIDE

Publication Number MAN0026726

Revision B.0

Affymetrix, Inc.

3450 Central Expressway

Santa Clara, CA 95051

The information in this guide is subject to change without notice.

DISCLAIMER:

TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL,

INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT,

INCLUDING YOUR USE OF IT.

Revision history: MAN0026726

Important Software Licensing Information

Your installation and/or use of this GeneChip Data Collection software is subject to the terms and conditions contained in the End User

License Agreement (EULA) which is incorporated within the GeneChip Data Collection software, and you will be bound by the EULA terms and

conditions if you install and/or use the software.

NOTICE TO PURCHASER: DISCLAIMER OF LICENSE

Purchase of this software product alone does not imply any license under any process, instrument or other apparatus, system, composition,

reagent or kit rights under patent claims owned or otherwise controlled by Life Technologies Corporation, either expressly, or by estoppel.

Legal entity

Affymetrix, Inc. | Santa Clara, CA 95051 USA | Toll Free in USA 1 800 955 6288

European Representative

Life Technologies Europe B.V.

Kwartsweg 2

2665 NN Bleiswijk

The Netherlands

TRADEMARKS

All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.

Revision Date Description

B.0 August 2023 Updated images, Added Language Installer instructions and new Laser Safety statement.

A.0 May 2022 Initial release in Thermo Fisher Scientific document control system.

Contents

GeneChip Data Collection (GCDC) User Guide 3

CHAPTER 1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

About GCDC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

GCDC configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

GCDC workflow overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

How GCDC processes arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

How GCDC processes cartridge arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Registering the samples and arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Registering sample options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Washing and staining cartridge arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Running the scanners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Tracking gridding and CEL file generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

GCDC file types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Sample files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Log files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Customer support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

CHAPTER 2 Starting GCDC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Before using GCDC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Prerequisites that must be met . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Starting GCDC (with Fluidics and Scanner) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Launcher modules with GCDC Fluidics Control and GCDC Scan Control . . . . . . . . . . 13

Starting GCDC (Analysis only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Launcher modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Language installer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

CHAPTER 3 Setting up GCDC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

System Configurator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Installing and assigning fluidics stations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Naming stations and their modules (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Changing the connected scanner name (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Changing the data storage output path . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Changing languages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Installing Protocol/Library files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Installing library files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Installing protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

CHAPTER 4 Registering samples . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Cartridge array overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Quick registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Contents

GeneChip Data Collection (GCDC) User Guide 4

Batch registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Edit registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

CHAPTER 5 Fluidics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Fluidics control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Fluidics Control window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Master controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Station controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Status window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Running protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Priming the fluidics station . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Running a fluidics protocol on multiple stations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Protocol Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Labeling check boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Running fluidics on individual stations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Limiting the listed protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Resuming a fluidics protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Bypassing steps in a fluidics protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

CHAPTER 6 Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Scan control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Scanner window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Status window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Reviewing scanner information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Scanner Information window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Using the GeneChip Scanner 3000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Laser safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Electrical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Starting the scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Shutting down the scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Using the AutoLoader option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Starting the AutoLoader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Shutting down the scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Setting up the AutoLoader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Scanning probe arrays with AutoLoader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Setting defaults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Special scan options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Drop and scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Contents

GeneChip Data Collection (GCDC) User Guide 5

Stopping an AutoLoader run. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Adding cartridge arrays during a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Scanning a probe array in manual mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Using GCDC with the AutoLoader disabled . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Autorotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Terminating a scan run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

AutoLoader error messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

CHAPTER 7 Data Viewer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Viewer overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Using the viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Data Viewer window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

File display differences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

DAT files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

CEL files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

JPG files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Viewing failed control features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Array and grid types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Review window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Enabling/Disabling the Review window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Updating the list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Changing the filter settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Filtering by date (since workflow ran) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Displaying only errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Filtering by other parameters displayed in the review window . . . . . . . . . . . . . . . . . . . 63

Changing the other settings of the workflow review window . . . . . . . . . . . . . . . . . . . . . . 64

Using the review window to open files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Displaying a listed DAT file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Sorting the list for a particular parameter value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Selecting columns for display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Using the open dialog window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Displaying multiple files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Displaying a specific image while multiple are open . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Displaying the full path to a displayed file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Changing the display of the image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Displaying hidden controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Examining different parts of the image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Zooming in on a selected image area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Zooming and image in and out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Viewing different areas of a zoomed image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Reseting a zoomed image size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Adjusting the colors and contrast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Switching between gray scale and pseudo color displays . . . . . . . . . . . . . . . . . . . . . . 70

Contents

GeneChip Data Collection (GCDC) User Guide 6

Changing the contrast range of an image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Using Autoscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Changing the grid and intensity display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Displaying cell intensity data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Displaying/Hiding cell intensity data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Displaying cell centers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Displaying the grid corners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Changing settings for the grid display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Saving image display options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Learning about the image file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

For DAT files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

For CEL files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

Expanding/Collapsing a component . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

Sorting data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

Grid information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

Checking the grid alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

Aligning the main grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

Viewing the main grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Fixing an alignment issue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Running the gridding algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Running the alignment algorithm on an array that uses a single grid . . . . . . . . . . . . . . 77

Aligning the grid manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Aligning sub-grids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Running the sub-grid alignment algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Running only the sub-grid alignment algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Manually aligning the sub-grids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Navigating from sub-grid to sub-grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Highlighting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Stepping through all sub-grids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Stepping only through the misaligned grids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Aligning a failed sub-grid manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Exporting images in other formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Copying images to the computer clipboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Creating a JPG file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Viewing the JPG file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Opening a JPG in the Windows Picture and Fax Viewer . . . . . . . . . . . . . . . . . . . . . . . . 87

Changing settings for the JPG conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

APPENDIX A Networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Network functionality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Workstation 1: GCDC Analysis Only . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Workstation 2: GCDC FS450 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Workstation 3: GCDC GCS3000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Contents

GeneChip Data Collection (GCDC) User Guide 7

Sample configurations for GCDC with network functionality . . . . . . . . . . . . . . . . . . . . . . . . 90

Linked instrument control systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Computer roles in linked control systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Scanner system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Required installed software for scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Tasks performed using the IC Scanner Workstation . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Fluidics system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Required installed software for fluidics system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Other required fluidics system requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Tasks performed using the IC Fluidics Workstation . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Network storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Computer roles for network storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Network data storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

GCDC IC workstations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

Local analysis workstation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

Local lab computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94

Setting up Windows networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94

Sharing and security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94

Changing the data storage output path . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

Assigning a data storage path on a network folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

APPENDIX B Monitoring instruments using the cloud . . . . . . . . . . . 97

Creating a cloud account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

Adding users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

Connecting to an instrument remotely . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

Smart phone (Android OS 5.0+ and iOS 9.0+ only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

Non-smart phone users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

Managing users (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

Viewing the instrument status in detail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

APPENDIX C Viewing upload errors. . . . . . . . . . . . . . . . . . . . . . . . . 102

Upload activity viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

APPENDIX D Collecting logs and editing protocols . . . . . . . . . . . . 103

Log collector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Protocol editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

GeneChip Data Collection (GCDC) User Guide 8

1Introduction

About GCDC

The development of microarray technology means that researchers can now perform

more experiments and collect more data from each experiment than ever before. As

a result, researchers need to analyze this data, which presents new challenges for the

researchers and the software they use.

GeneChip Data Collection (GCDC) enables you to process cartridge arrays, capture

images of the intensity data using a solid-state laser, and extract the intensity data

from the images for use by probe level analysis software.

Use the GCDC software to:

Enter and organize information about the sample and GeneChip probe arrays.

Control the instruments used to process probe arrays and collect the intensity

data.

Track the progress of an array through the array processing workflow.

Work seamlessly with other tools for downstream analysis.

GCDC configurations

GCDC and GeneChip Scanner 3000 system (GCS3000 and FS450)

GCDC (Analysis Only)

IMPORTANT! The GCDC software has been validated for use with your Operating System’s built-

in Windows Defender anti-virus software. Using other anti-virus software is not recommended, as

it may cause incompatibility issues.

IMPORTANT! The screen captures used in this User Guide are in English (US). If another

language is used, these screen captures are for reference purposes only.

GeneChip Data Collection (GCDC) User Guide 9

Chapter 1 Introduction

GCDC workflow overview 1

GCDC workflow overview

How GCDC

processes arrays

GCDC is used to process the arrays in your experiments. The recommended workflow

for processing cartridge arrays enables you to include data about the sample and

experiment, then easily track its processing steps.

1. Sample/Array Registration: Creation of ARR file with sample information.

2. Hybridization of Sample to Cartridge: This is not controlled by GCDC.

3. Fluidics Station: Washing and Staining of the Array after hybridization is

complete.

4. Scanner: Array is scanned, and DAT file of the image is created.

5. Data Viewer: Review grid alignment, manually adjust the grid, recreate CEL files

if needed

6. Analysis: CEL file signal intensities are generated by GCDC. Analysis of these

files is performed using Thermo Fisher Scientific software and/or 3rd party

software packages.

How GCDC

processes

cartridge arrays

In the array processing workflow for cartridge arrays, you create a sample file as the

first step, assigning sample attributes and the array barcode to the sample. You then:

1. Hybridize the sample to the array

2. Wash and stain the array

3. Scan the array to create Image data (DAT) file

GCDC aligns a grid on the DAT file and computes the intensity data generating a CEL

intensity file for the array. The CEL file is created by the GCDC software for the sample

and is used by subsequent data analysis software packages.

Registering the samples and arrays

In GCDC, the Sample file is the beginning of the data chain for a given experiment. The

sample information is stored in a Sample file with an ARR extension. The arrays used

in analysis and data files produced by analysis are linked to this Sample File.

The information about the sample(s) and experiment(s) are collected as attributes.

Registering sample options

GCDC provides multiple ways to create Sample files. To select the best one for your

operation, evaluate:

The number of arrays you are going to be processing.

Whether you want to enter sample attributes during registration.

Whether you want to enter attributes at a later time.

For example:

Batch Registration enables you to create a group of Sample files for cartridge

arrays; you can assign attributes to each Sample file, along with one or more

arrays.

GeneChip Data Collection (GCDC) User Guide 10

Chapter 1 Introduction

GCDC workflow overview 1

Quick Registration creates sample files for cartridge arrays, each with a single

array and attributes.

Edit Registration enables updating or editing of a sample’s attributes or adding

attributes or barcode information for the sample.

User attributes allow notes for a sample file to be created during registration of

a sample and array.

The Drop and Scan feature enables you to create a sample file for an array when

the array is scanned. Drop and Scan is available for:

Cartridge arrays (see "Drop and scan" on page 50)

Washing and staining cartridge arrays

Note: Hybridization of cartridge arrays is not controlled using the GCDC software.

The Fluidics Station 450 (FS450) is used to wash and stain the GeneChip arrays.

The GCDC Fluidics Control software is used to control the FS450. A workstation with

GCDC Fluidics Control software and a Sealevel card installed can control up to eight

fluidics stations.

Running the scanners

The array is scanned after hybridization, washing, and staining, using one of the

following scanners:

GeneChip Scanner 3000 (GCS3000) (scans one chip only)

GCS3000 with Autoloader (load up to 48 chips for scanning without operator

attention)

Note: The GCDC Scan Control software is used to control the scanner.

Tracking gridding and CEL file generation

After the array has been scanned, GCDC:

Aligns a grid on the Image (DAT) file to identify the probe cells.

Computes the probe cell intensity data for the array and creates a CEL file.

Generates JPG and RPT files.

The GCDC Data Viewer enables you to track the progress of this step in the workflow

and manually correct gridding problems, if necessary.

GeneChip Data Collection (GCDC) User Guide 11

Chapter 1 Introduction

GCDC file types 1

GCDC file types

Different types of information are collected by GCDC in different types of files:

Information about the sample and experiment are collected in Sample files (see

"Sample files", below)

Probe array data generated during scanning and processing are collected in Data

files of various types.

Audit and Log files contain information about array processing and other

processes (see "Log files" on page 11)

Globally Unique Identifiers (GUIDs) are used to track the relationships between

Sample files, physical arrays, and Data Files.

Sample files The Sample (ARR) file collects two types of information:

Sample Attributes: information that you can use to interpret the experimental data.

It can include information about the sample itself, the experimental conditions, or

other information you may find useful.

Array Information: Information about the array(s) used with the sample. More than

one array can be associated with the sample. This is useful for tracking replicates;

in addition, it can be used to simplify tracking data for multi-chip arrays. Each array

is assigned an array name during registration. The array name is used to identify

the DAT, CEL, and CHP data files that are generated during analysis.

Log files Log files are produced by different GCDC components. The logs provide a record of

the tasks performed by different components, such as the migration tools and the

installer. Log files can provide valuable troubleshooting information and may be

requested by your Support person. To use log files, see "Log collector" on page

103.

Customer support

Visit thermofisher.com/support for the latest in service and support, including:

Worldwide contact telephone numbers

Product support, including:

Product FAQs

Software, patches, and updates

Order and web support

Product documentation, including:

User guides, manuals, and protocols

GeneChip Data Collection (GCDC) User Guide 12

2Starting GCDC

Before using GCDC

Prerequisites that

must be met

An image with Windows 10 Enterprise 2019 LTSC and the instrument control

software must be used. The Analysis Only software can be installed by the user on

Windows 10 Professional OS.

The necessary GCDC components are installed.

Libraries are installed for the probe array types you want to process.

The correct fluidics scripts are installed for the probe array types you want to

process. Note: Fluidics scripts are included as part of the image of the system and

will be pre-installed on the system.

If using remote network data storage or linked instrument control systems, you

need to perform additional configuration. See Appendix A, "Networking" on

page 89.

If you need the software to be in another language, see "Language installer" on

page 15.

Do not remove these pre-installed system components:

.Net FrameWork 4.8

SQL Server 2012 Express

Microsoft Visual C++ 2013 Redistributable

MS Access DBEngine 2010 on Windows 10

IMPORTANT! Before running GCDC for a particular GeneChip Array, you must have the library

files for that array type installed on your computer.

IMPORTANT! The GCDC software has been validated for use with your Operating System’s built-

in Windows Defender anti-virus software. Using other anti-virus software is not recommended, as

it may cause incompatibility issues.

IMPORTANT! Windows updates should not be installed while samples are being processed.

Automatic updates must be turned off. Install updates manually when the system is not in use.

GeneChip Data Collection (GCDC) User Guide 13

Chapter 2 Starting GCDC

Starting GCDC (with Fluidics and Scanner) 2

Starting GCDC (with Fluidics and Scanner)

1. Click Start →Thermo Fisher Scientific → GCDC Launcher - RUO or double-

click on its Desktop shortcut.

Note: To start the Analysis Only version of GCDC, go to See “Starting GCDC

(Analysis only)” on page 14.

The Launcher appears. (Figure 1)

The GCDC Launcher window appears containing all the necessary software

components to process an array. It includes the software tools for sample

registration, instrument control, installation of library and protocol files,

configuring data output files, data viewing, and log collection.

Additional GCDC components work behind the scenes and include an Indexer. The

Indexer is a service that tracks the files of the arrays that are being run and runs

automatically. Note: There may be instances when its configuration settings need to

be changed. Make sure you contact Support before changing any Indexer settings.

Launcher modules with GCDC Fluidics Control and GCDC Scan Control

Fluidics: Runs the Fluidics Station 450.

Scanner: GeneChip Scanner 3000 (GCS3000) with Autoloader and scanner

software.

Array Registration: Use to registering samples.

Data Viewer: For viewing image data, workflow status, and performing manual

gridding.

IMPORTANT! Data generated for all arrays (including Dx arrays) will be tagged as RUO. If you

are running Dx arrays, refer the GeneChip Data Collection Dx User Guide (P/N MAN0026725).

Figure 1 GCDC Launcher menu

GeneChip Data Collection (GCDC) User Guide 14

Chapter 2 Starting GCDC

Starting GCDC (Analysis only) 2

Install Protocol/Library: A Fluidics scripts and library files installation tool

required for processing arrays.

Log Collector: Used to collect log files from your system in cases when

troubleshooting is required.

Configurator: Installation of Fluidics Stations (and naming if desired), Scanner

(naming if desired), setup of data storage locations and Language selection

thermofisher.com: Link to website.

Support: Link to Support.

Help: PDF of User Guide (Acrobat Reader required)

About: GCDC version number.

Starting GCDC (Analysis only)

1. Click Start →Thermo Fisher Scientific → GCDC RUO Launcher - Analysis

Only or double-click on its Desktop shortcut.

The Launcher appears. (Figure 2)

Instrument Control (Fluidics and Scanner) are not available on the GCDC Analysis

Only Launcher, however, it does include the software tools for sample

registration, installation of library and protocol files, configuring data output files,

data viewing, and log collection.

Additional GCDC components work behind the scenes and include an Indexer. The

IMPORTANT! Data generated for all arrays will be tagged as RUO. If you are running Dx arrays,

refer the GeneChip Data Collection Dx User Guide (P/N MAN0026725).

Figure 2 GCDC Analysis Only Launcher menu

GeneChip Data Collection (GCDC) User Guide 15

Chapter 2 Starting GCDC

Language installer 2

Indexer is a service that tracks the files of the arrays that are being run and runs

automatically. Note: There may be instances when its configuration settings need to

be changed. Make sure you contact Support before changing any Indexer settings.

Launcher modules

Array Registration: Use to registering samples.

Data Viewer: For viewing image data, workflow status, and performing manual

gridding.

Install Protocol/Library: A Fluidics scripts and Library files installation tool

required for processing arrays.

Log Collector: Used to collect log files from your system in cases when

troubleshooting is required.

Configurator: Installation of Fluidics Stations (and naming if desired), Scanner

(naming if desired), setup of data storage locations and Language selection

thermofisher.com: Link to website.

Support: Link to Support.

Help: PDF of User Guide (Acrobat Reader required)

About: GCDC version number.

Language installer

The Language Installer is used to change GCDC from English (US) to a different

language that is available on your system.

1. Unzip 611406_GCDCLanguagePack.zip.

2. Run LanguageSchemaInstaller.exe.

A LanguageFileInstaller\LanguageSchemainstaller.exe window appears

confirming the XML and GLP files were installed successfully and what folder the

GLP file resides in.

3. Click on (upper right).

A menu appears.

4. Click Language Installer.

A Windows system message appears asking to allow the Language Installer to

make changes to the system.

5. Click Yes.

The Language Installer window appears. (Figure 3)

GeneChip Data Collection (GCDC) User Guide 16

Chapter 2 Starting GCDC

Language installer 2

6. Click the “...” button (upper right).

A Windows Explorer window appears.

7. Navigate to the GCDC Language Pack, locate the .GLP file, then click Open.

8. The available languages now appear, as shown in Figure 4.

9. Check the desired language check box(es) or click the All/None check box, then

click Install.

A message appears stating the languages were successfully installed.

10. Close the Language Installer window, then go to "Changing languages" on page

19 for instructions on how to activate your selected language.

Figure 3 GCDC Launcher menu - Language Installer window

Figure 4 Available languages

GeneChip Data Collection (GCDC) User Guide 17

3Setting up GCDC

System Configurator

Install and assign up to eight Fluidics stations.

Change the name of the connected Scanner.

Assign data output paths and their definitions.

Change the language of the software.

1. At the Launcher window, double-click on .

The System Configurator window appears. (Figure 5)

Installing and

assigning fluidics

stations

Use the Fluidics window tab (Figure 6) to install and assign up to eight Stations.

IMPORTANT! You must be logged in as an Administrator to use the System Configurator.

Figure 5 System Configurator

Figure 6 Fluidics tab window

GeneChip Data Collection (GCDC) User Guide 18

Chapter 3 Setting up GCDC

System Configurator 3

1. Make sure all Stations are ready and connected.

2. Click on the Number of Stations to Install drop-down to select the number of

Stations you want to use, then click Save.

A dialog window appears confirming the Station(s) were installed successfully.

3. Check the Number of Stations Installed field to confirm the Station(s) were

installed.

Naming stations and their modules (optional)

By default, Stations are numbered 1 - 8 and their modules 1 - 4. These defaults can

be renamed.

1. Click on the Selected Station drop-down to select the Station you want to

rename.

The Selected Station ID field appears displaying the Station’s default name.

2. Click inside this field to enter a new name.

3. Click inside each Module ID field to enter a new name.

4. Click Save.

A dialog window appears confirming the stations/modules were saved

successfully.

5. Click OK.

6. Your entered Station and Module names are now displayed in the Fluidics

interface window, as shown in Figure 7.

Changing the

connected

scanner name

(optional)

1. Click the Scanner tab.

The Scanner tab window appears. (Figure 8)

2. Click inside the Scanner 1 field, enter a Scanner name, then click Save.

A Success dialog window appears confirming the name change.

3. Click OK.

Figure 7 Fluidics interface window

Figure 8 Scanner tab window

GeneChip Data Collection (GCDC) User Guide 19

Chapter 3 Setting up GCDC

System Configurator 3

Changing the

data storage

output path

1. Click the Data Storage tab.

The Data Storage tab window appears. (Figure 9)

Note: The (grayed out) Default Data Path cannot be changed.

2. Click Choose Folder.

An Explorer window appears.

3. Navigate to the Data Output folder (path) you want, then click Open.

Note: The folder you choose can reside on a local or network drive.

Your new path is displayed.

4. Click Apply to activate your new folder path.

The Status field confirms your updated path was completed successfully.

Changing

languages

1. Click the Language Translation tab.

The Language Translation tab window appears. (Figure 10)

Figure 9 Data Storage tab window

GeneChip Data Collection (GCDC) User Guide 20

Chapter 3 Setting up GCDC

Installing Protocol/Library files 3

2. Click the Available Languages drop-down to select a new language.

A Success dialog window appears stating the application must be restarted for

the new language to take effect.

3. Click OK.

Installing Protocol/Library files

Note: If you are using non-legacy library files, you must first extract the zip folder and

run the provided executable.

1. At the Launcher window, double-click on .

The Library/Protocol window appears. (Figure 11)

This Library window is used to install files for processing the arrays, such as, scan

file parameters, grid parameter files, etc.

Note: Always download files in an easily accessible folder.

Figure 10 Language Translation tab window

Figure 11 Library/Protocol window

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