Thermo Fisher Scientific SeqScreener Gene Edit Confirmation App User guide

Brand: Thermo Fisher Scientific

Model: SeqScreener Gene Edit Confirmation App

Type: User guide

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

SeqScreener Gene Edit Conﬁrmation App

USER GUIDE

Publication Number MAN0019455

Revision A.0

Life Technologies Corporation | 200 Oyster Point Blvd | South San Francisco, California 94080 USA

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Revision history: Pub. No. MAN0019455

Revision Date Description

A.0 19 March 2021 New document for the SeqScreener Gene Edit Conﬁrmation App.

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Contents

■CHAPTER 1 About the SeqScreener Gene Edit Conﬁrmation App on

Thermo Fisher™ Connect ........................................................... 5

Software overview ............................................................... 5

Example workﬂow used with the SeqScreener Gene Edit Conﬁrmation App ............ 6

Network and password security requirements ...................................... 7

Network conﬁguration and security ........................................... 7

Password security .......................................................... 7

■CHAPTER 2 Get started with the SeqScreener Gene Edit

Conﬁrmation App ................................................................... 8

Compatible instruments .......................................................... 8

Browser compatibility ............................................................ 8

Customize project and application settings ........................................ 9

■CHAPTER 3 Start a new project ................................................. 12

Import sample and control ﬁles .................................................. 12

Complete sample information and analyze ........................................ 14

■CHAPTER 4 View results .......................................................... 18

View results summary .......................................................... 18

Results overview table ..................................................... 20

View detailed results for a project ................................................ 22

Results details: Overview (plate view) ........................................ 23

Results details: Indel frequency chart ........................................ 24

Results details: Donor to control alignment ................................... 25

Results details: Sequencing traces .......................................... 26

Editing grade categories ........................................................ 27

View past results ............................................................... 28

SeqScreener Gene Edit Conﬁrmation App User Guide 3

■CHAPTER 5 Export results ....................................................... 29

Export the Results overview table ................................................ 29

Export results details ........................................................... 30

Results ﬁles ................................................................... 31

■APPENDIX A Software screen descriptions ..................................... 33

Setup tab ..................................................................... 33

Results tab .................................................................... 33

Details tab, Overview screen .................................................... 34

Details tab, Indel frequency chart screen ......................................... 34

Details tab, Donor to control alignment screen .................................... 34

Details tab, Sequencing traces screen ........................................... 35

■APPENDIX B Documentation and support ...................................... 36

Customer and technical support ................................................. 36

Limited product warranty ........................................................ 36

Contents

4SeqScreener Gene Edit Conﬁrmation App User Guide

About the SeqScreener Gene

Edit Conﬁrmation App on Thermo

Fisher™ Connect

■Software overview ..................................................................... 5

■Example workﬂow used with the SeqScreener Gene Edit Conﬁrmation App ................... 6

■Network and password security requirements ............................................. 7

The SeqScreener Gene Edit Conﬁrmation App (SGC) is an application available through Thermo Fisher™

Connect that can be used to determine the spectrum and frequency of targeted mutations generated in

a pool of cells by genome editing tools such as CRISPR-Cas9. Use the SGC app to screen and validate

gene editing results obtained using Capillary Electrophoresis (CE) sequencing technology.

The SGC app includes the following features:

•An algorithm that accurately reconstructs the spectrum of Indels from the sequence traces and

generates a report

•A report output that identiﬁes the detected Indels and their frequencies

•Detection of designed mutations generated by homologous recombination using a donor template

•Compatibility with both knock-in and knock-out experiments

•Batch import capability

•Pool screening and clonal screening analyses

Software overview

The SeqScreener Gene Edit Conﬁrmation App (SGC) user interface provides an easy-to-follow workﬂow

to facilitate the analysis of gene editing results.

1 2 3

1Set up your project and import ﬁles for analysis

2View gene editing results for all edited sample ﬁles included in an analysis

3View in-depth details for a speciﬁc result

SeqScreener Gene Edit Conﬁrmation App User Guide 5

When you ﬁrst access the SGC app, you are directed to the Setup tab, where you can start a new

project. Project setup includes uploading at least 1 control ﬁle and 1 sample ﬁle, then providing

information that is required for analysis, such as gRNA target sequence and donor sequence. For

detailed instructions on how to set up your project, see Chapter 3, “Start a new project”.

After you create your project and run the analysis, the software populates the results in the Results tab

and the Details tab. The Results tab summarizes the editing eciency results for all edited sample ﬁles

included in an analysis. The Details tab provides an interactive platform for viewing detailed results for

each sample, including visualization tools such as plate view results overview, Indel Frequency Chart,

Donor to Control Alignment, and Sequecing Traces.

•For more information on the results summary, see “View results summary” on page 18.

•For more information on visualizing results for each sample, see “View detailed results for a project”

on page 22.

Example workﬂow used with the SeqScreener Gene Edit

Conﬁrmation App

From experiment set up to result

Set up experiments on Thermo Fisher™ Connect

Set up experiments on your capillary electrophoresis (CE) Sanger sequencing instrument

Use the Plate Manager software available through Thermo Fisher™ Connect or set up experiments directly

on your CE instrument. Refer to the software Help or the instrument User Guide for guidance.

Run samples on a CE Sanger sequencing instrument

For instructions on running samples on a CE instrument, refer to the user guide speciﬁc to your

instrument.

Set up your project and import ﬁles for analysis in SeqScreener Gene Edit Conﬁrmation App (see

Chapter 3, Start a new project)

Use the Setup tab to start a new project, upload sample and control ﬁles, enter sample information, and

launch an analysis.

View the summary of results (see View results summary)

AND/OR

View detailed results (see View detailed results for a project)

View the summary of editing eciency results in the Results tab and use the interactive visualization tools

in the Details tab to evaluate the editing eciency quality for each sample in a project.

Chapter 1 About the SeqScreener Gene Edit Conﬁrmation App on Thermo Fisher™ Connect

Example workﬂow used with the SeqScreener Gene Edit Conﬁrmation App

6SeqScreener Gene Edit Conﬁrmation App User Guide

(continued)

From experiment set up to result

Export results (see Chapter 5, Export results)

Export raw results, analysis summary PDF report, or presentation-ready images and printable graphics to

share your results.

Network and password security requirements

Network conﬁguration and security

The network conﬁguration and security settings of your laboratory or facility (such as ﬁrewalls, anti-

virus software, network passwords) are the sole responsibility of your facility administrator, IT, and

security personnel. This product does not provide any network or security conﬁguration ﬁles, utilities, or

instructions.

If external or network drives are connected to the software, it is the responsibility of your IT personnel

to ensure that such drives are conﬁgured and secured correctly to prevent data corruption or loss. It

is the responsibility of your facility administrator, IT, and security personnel to prevent the use of any

unsecured ports (such as USB, Ethernet) and ensure that the system security is maintained.

Password security

Thermo Fisher Scientiﬁc strongly recommends that you maintain unique passwords for all accounts in

use on this product. All passwords should be reset upon ﬁrst sign in to the product. Change passwords

according to your organization's password policy.

It is the sole responsibility of your IT personnel to develop and enforce secure use of passwords.

Chapter 1 About the SeqScreener Gene Edit Conﬁrmation App on Thermo Fisher™ Connect

Network and password security requirements 1

SeqScreener Gene Edit Conﬁrmation App User Guide 7

Get started with the SeqScreener

Gene Edit Conﬁrmation App

■Compatible instruments ................................................................ 8

■Browser compatibility .................................................................. 8

■Customize project and application settings ............................................... 9

Compatible instruments

The SeqScreener Gene Edit Conﬁrmation App is compatible with the following instruments.

•3500/3500xL Genetic Analyzer

•3730/3730xl DNA Analyzer

•Applied Biosystems™ SeqStudio™ Genetic Analyzer

Browser compatibility

SeqScreener Gene Edit Conﬁrmation App can be operated on all modern web browsers such as

Google™ Chrome™, Microsoft™ Edge, Apple™ Safari™, and Firefox™.

SeqScreener Gene Edit Conﬁrmation App does not support Microsoft™ Internet Explorer™.

8SeqScreener Gene Edit Conﬁrmation App User Guide

Customize project and application settings

In the SeqScreener Gene Edit Conﬁrmation App (SGC), you can set default project save location on

Thermo Fisher™ Connect and deﬁne how you want your projects to be named.

If you need to modify advanced settings such as alignment window, decomposition window, indel size

range, and contribution threshold, contact your FAS before making any changes.

1. In the top right corner of the screen, click (Settings).

2. In the Settings window, modify settings as needed.

Setting Description

Save location Select the default location on Thermo Fisher™

Connect where you want to save SGC projects.

1. In the left navigation pane, click Save

Location.

The default save location is displayed in the

pane on the right.

2. Select the folder where you want to save

your projects, or click (New Folder)

to create a new folder on Thermo Fisher™

Connect.

Note: If you have a lot of folders, you can

enter a search term in the Search ﬁeld to

locate the folder of interest.

3. Click to select the folder that you want to set

a new default save location.

4. Click Save.

If you need to delete, rename, or rearrange folders,

you can do so through Thermo Fisher™ Connect.

For more information, see the Thermo Fisher™

Connect Help.

Naming convention You can customize your project naming

convention by arranging project name attributes

and adding custom attributes to the project

name as needed. Project name can be up to

100 characters in length.

Chapter 2 Get started with the SeqScreener Gene Edit Conﬁrmation App

Customize project and application settings 2

SeqScreener Gene Edit Conﬁrmation App User Guide 9

Setting Description

1. In the left navigation pane, click Naming

Convention.

The default name convention is displayed,

showing an example preview name.

2. Click and drag an attribute to rearrange the

name convention.

3. (Optional) In the Alternative attributes

section, click to add another attribute to

your project naming convention.

4. (Optional) In the Alternative attributes

section, in the Add custom text ﬁeld, enter

a name for a custom attribute, then click

to add the custom attribute to your naming

convention. If needed, click to edit your

custom attribute.

Note: The custom attribute ﬁeld accepts all

alphanumeric characters. Special characters

% ? | ; : , ! @ $ < > / \ " ' ` ~ [ ] { } = ^ are not

allowed.

5. Click Save.

Alignment window IMPORTANT! Do not change the alignment

window settings. If modiﬁcations are needed,

contact your FAS before making any changes.

The alignment window deﬁnes the maximum size

in base pairs (bps) of the sequence window used

in the control and test sample alignment. By

default, the SGC algorithm uses the maximum

window size possible.

1. In the left navigation pane, click Advanced

Settings.

2. In the Alignment Window pane, move the

slider to the desired window size.

3. Click Save.

4. If needed, click Restore to default settings

to restore advanced settings to default

values.

Decomposition window IMPORTANT! Do not change the

decomposition window settings. If modiﬁcations

are needed, contact your FAS before making any

changes.

Chapter 2 Get started with the SeqScreener Gene Edit Conﬁrmation App

Customize project and application settings

10 SeqScreener Gene Edit Conﬁrmation App User Guide

Setting Description

The decomposition window deﬁnes the maximum

size, in bps, of the sequence window used in

decomposition. By default, the SGC algorithm

uses the maximum window size possible.

1. In the left navigation pane, click Advanced

Settings.

2. In the Decomposition Window pane, move

the slider to the desired window size.

3. Click Save.

4. If needed, click Restore to default settings

to restore advanced settings to default

values.

Indel size range IMPORTANT! Do not change the indel size

range settings. If modiﬁcations are needed,

contact your FAS before making any changes.

The maximum and minimum sizes, in bps,

of all insertions and deletions modelled in

decomposition. The default size range is 0–10

bps.

1. In the left navigation pane, click Advanced

Settings.

2. In the Indel Size Range pane, move the

sliders to deﬁne the desired range.

3. Click Save.

4. If needed, click Restore to default settings

to restore advanced settings to default

values.

Contribution threshold IMPORTANT! Do not change the contribution

threshold settings. If modiﬁcations are needed,

contact your FAS before making any changes.

The contribution threshold uses the editing

eciency value of edited sequences. Edited

sequences below this threshold are excluded from

diversity calculations.

1. In the left navigation pane, click Advanced

Settings.

2. In the Contribution threshold pane, move

the slider to deﬁne the desired range.

3. Click Save.

4. If needed, click Restore to default settings

to restore advanced settings to default

values.

Chapter 2 Get started with the SeqScreener Gene Edit Conﬁrmation App

Customize project and application settings 2

SeqScreener Gene Edit Conﬁrmation App User Guide 11

Start a new project

■Import sample and control ﬁles ......................................................... 12

■Complete sample information and analyze .............................................. 14

Use the Setup tab to start a new project, upload sample and control ﬁles, enter the required sample

information, and proceed to analysis. When you open the SeqScreener Gene Edit Conﬁrmation App

from Thermo Fisher™ Connect, the Setup tab opens by default. If you are viewing results from the

Results tab or the Details tab and would like to start a new project or add more samples to an existing

project, you can go back to project setup by clicking the Setup tab.

Note: When you start a new project, the project name is automatically assigned based on the naming

convention designated during application set up (out-of-box) or in Settings. For more information,

including how to customize your project naming convention, see “Customize project and application

settings” on page 9.

Import sample and control ﬁles

The ﬁrst step in setting up a new project is uploading edited sample ﬁles that you want to analyze and

their corresponding control ﬁles. You must upload at least 1 edited sample ﬁle and 1 control ﬁle for each

project. The SeqScreener Gene Edit Conﬁrmation App requires all ﬁles to be in AB1 format. Folders and

ZIP format ﬁles are also accepted.

File requirements:

•A maximum of 2400 experiment ﬁles and 2400 control ﬁles can be added to a single project.

•Individual AB1 ﬁles cannot exceed 3 MB size per ﬁle.

•ZIP format ﬁles cannot exceed 1 GB per ﬁle.

•Empty ﬁles (0 KB) are not accepted.

•Edited sample ﬁles are ﬂagged as duplicate if one or more of the following attributes are the same

between ﬁles: Plate name, Well ID, Data collection time, Instrument name.

1. If you have an analysis open and you want to start a new analysis, click Start new project (or

Actions4Start new project) to clear all previous project data. Otherwise, proceed to step 2.

2. In the Setup tab, in step 2, select the screening type.

•Pool screening – select pool screening if you want to assess the overall editing eciency of a

gene editing experiment. Pool screening analyzes overall gene editing eciency and identiﬁes

gRNA designs that would be suitable for further clonal isolation.

•Clonal screening – select clonal screening when sequencing samples from a single clone.

This secondary screening step identiﬁes the clone that has the desired gene edit and the

actual sequence of the edited gene.

12 SeqScreener Gene Edit Conﬁrmation App User Guide

Note: Screening type selection determines the criteria for the assignment of clonal grades. For

more information, see “Editing grade categories” on page 27.

3. In step 3, import at least 1 edited sample ﬁle and 1 control ﬁle for each project.

Option Description

Import ﬁles from your local storage 1. In the Import edited sample ﬁle(s) pane,

click import ﬁle(s) or import folder.

2. In the Import location dialog, click

Computer, then browse to the location of the

experiment ﬁles in your local storage.

3. Select one or more ﬁles of interest, then click

Open to import the selected ﬁles.

4. In the Import control ﬁle(s) pane,

repeat steps 1–3 to import one or more

corresponding control ﬁles.

Drag and drop ﬁles from your local storage 1. Open the folder that contains the experiment

ﬁles or folders on your local storage device.

2. From the local ﬁles folder, select one or

more sample ﬁles or folders, then click and

drag the selected ﬁles into the Import edited

sample ﬁle(s) pane.

3. Select one or more control ﬁles, then click

and drag the selected ﬁles into the Import

control ﬁle(s) pane.

Import ﬁles from Thermo Fisher™ Connect 1. In the Import edited sample ﬁle(s) pane,

click import ﬁle(s) or import folder.

2. In the Import location dialog, click

Thermo Fisher™ Connect, then browse to

the location of the experiment ﬁles in your

Thermo Fisher™ Connect account.

3. Select one or more experiment ﬁles, then

click Import to import the selected ﬁles.

4. In the Control ﬁle(s) import pane,

repeat steps 1–3 to import one or more

corresponding control ﬁles.

When the sample and control ﬁles are ﬁnished uploading, the SeqScreener Gene Edit Conﬁrmation App

validates the ﬁles and populates the list of imported ﬁles in the samples table.

Before you proceed to analysis and results, you must complete the required sample information in the

table. For more information, see “Complete sample information and analyze” on page 14.

Chapter 3 Start a new project

Import sample and control ﬁles 3

SeqScreener Gene Edit Conﬁrmation App User Guide 13

Complete sample information and analyze

To pre-populate the samples table with sample and control ﬁles, import at least 1 sample ﬁle and

1 control ﬁle. For more information, see “Import sample and control ﬁles” on page 12.

The entire analysis workﬂow can be completed from the SeqScreener Gene Edit Conﬁrmation App

by entering the required ﬁle information directly into the samples table. For batch ﬁle imports with

multiple plates and large number of samples (for example, ≥10 samples), you can also import sample

information using an XLSX ﬁle.

1. In the Setup tab, in step 4, complete the samples table by manually entering the sample

information into the provided ﬁelds or importing the batch sample information using an XLSX ﬁle.

•Manually enter sample information into the samples table.

Column Description

Control ﬁle In the Control ﬁle column, in the row of each

sample, select the control ﬁle that corresponds

to the sample from the dropdown list.

gRNA target sequence (No PAM) In the gRNA target sequence (No PAM)

column, in the row of each sample, enter

1 target sequence in the provided ﬁeld. Target

sequence can be 17–23 nucleotides in length

and must contain A, T, G, C, or U characters

only. Do not include 3-bp sequence of the

protospacer adjacent motif (PAM).

Donor sequence (required for knockin

experiments)

In the Donor sequence column, in the row of

each sample, enter 1 donor sequence in the

provided ﬁeld. Donor sequence must contain A,

T, G, C, or U characters only.

Note: You can copy the entered ﬁle information to multiple consecutive rows by clicking

the bottom right corner of a cell that you want to copy and dragging down or up to add

the information to one or more neighboring cells. You can also double click the bottom right

corner of a cell to copy the entry to all cells below.

Chapter 3 Start a new project

Complete sample information and analyze

14 SeqScreener Gene Edit Conﬁrmation App User Guide

•Alternatively, click download (or click Actions4Blank template download) to download a

blank XLSX mapping ﬁle template, use the template to enter the required mapping information,

then save the ﬁle to your local storage. Click import to import the new XLSX ﬁle that

contains your sample information (see Figure 1, callouts 6 and 7).

Mapping information includes the following attributes:

–Plate (Optional)

–Well (Optional)

–Experiment edited sample ﬁle (Required)

–Control ﬁle (Required)

–gRNA target sequence (no PAM)

(Required)

–Donor sequence (Required for KI analysis)

2. (Optional) Sort the samples table.

•Click the arrow in a header of a column to sort the samples according to the column category.

•If you imported more than one plate, click (Filter) in the Plate column header, then select

a plate from the dropdown list to display only the ﬁles in the selected plate. To view all plates,

select View all (default).

Chapter 3 Start a new project

Complete sample information and analyze 3

SeqScreener Gene Edit Conﬁrmation App User Guide 15

3. (Optional) If needed, modify the samples table.

Action Description

Delete one edited sample ﬁle Click to select the row for a ﬁle that you want to

delete, then click (Delete) on the left side of

the table (see Figure 1, callout 4).

Delete multiple edited sample ﬁles 1. Select ﬁles that you want to delete using one

of the following strategies:

•Click in a row, then drag the mouse to

select multiple adjacent ﬁles.

•Click in a row, then Shift+Click to select

multiple adjacent ﬁles.

•Ctrl+Click in a row of each individual ﬁle

to select multiple non-adjacent ﬁles.

2. Above the top right corner of the table, click

(Actions)4Delete ﬁle(s) (see Figure 1,

callout 9).

Clear sample information for selected ﬁles 1. Select ﬁles that you want to modify using one

of the following strategies:

•Click in a row, then drag the mouse to

select multiple adjacent ﬁles.

•Click in a row, then Shift+Click to select

multiple adjacent ﬁles.

•Ctrl+Click in a row of each individual ﬁle

to select multiple non-adjacent ﬁles.

2. Above the top right corner of the table,

click (Actions)4Clear selected text (see

Figure 1, callout 9)..

Clear sample information for all ﬁles Click (Actions)4Clear all (see Figure 1,

callout 9).

Clear all setup content and ﬁles Click Start new project.

Chapter 3 Start a new project

Complete sample information and analyze

16 SeqScreener Gene Edit Conﬁrmation App User Guide

5 8 10

Figure 1 Setup tab

1Screening type selection menu

2File import tools: Edited sample ﬁle(s) import and Control

ﬁle(s) import panes

3Samples table

4Delete the selected ﬁle

5Erase all ﬁles and start a new project

6Import an XLSX ﬁle that contains mapping information

7Download a blank XLSX mapping ﬁle template

8Save the project to Thermo Fisher™ Connect

9Actions for modifying the samples table, including deleting

ﬁles and clearing sample data

10 Save the project to Thermo Fisher™ Connect and analyze

4. (Optional) Click Actions4Export mapping ﬁle to export the samples table in XLSX format for

future use.

5. Click Analyze.

STOPPING POINT Alternatively, you can click Save to save your project setup, including all the

information that you entered into the samples table. You can come back later to complete the table

and analyze. For more information, see “View past results” on page 28.

The analysis results data and all sample information is automatically saved to your Thermo Fisher™

Connect account, in a folder that is speciﬁed in the Save location settings. For more information,

see “Customize project and application settings” on page 9.

Upon successful analysis, the Results tab automatically opens, displaying the Results overview table

that lists editing eciency summary for all samples.

If you want to edit samples or add new samples to the project after you analyzed the original set of

samples, you can go back to the Setup tab, make any necessary changes, then re-analyse.

Chapter 3 Start a new project

Complete sample information and analyze 3

SeqScreener Gene Edit Conﬁrmation App User Guide 17

View results

■View results summary ................................................................. 18

■View detailed results for a project ....................................................... 22

■Editing grade categories ............................................................... 27

■View past results ..................................................................... 28

The SeqScreener Gene Edit Conﬁrmation App populates results in the Results tab and the Details

tab. The Results tab compiles the editing eciency results in Results overview table that includes

information such as editing grade, whether an edit is a knock-in (KI) or knock-out (KO) mutation, Model

ﬁt, Editing %, Frameshift %, and Edit diversity. The Details tab provides an interactive platform for

visualizing results for each sample, including tools such as plate view results overview, Indel frequency

chart, Donor to control alignment, and Sequencing traces.

View results summary

When the analysis of edited sample ﬁles is complete, editing eciency results are summarized in the

Results tab, in the Results overview table. The Results tab opens by default upon the completion of

analysis.

The Results overview table provides the list of results for all edited sample ﬁles that were analyzed in a

project. You can quickly ﬁnd results of interest by sorting the table according to each column category.

You can also annotate candidates of interest by adding sample-speciﬁc notes as well as include

project-speciﬁc notes for future review. For a description of each column in the Results overview table,

see “Results overview table” on page 20.

From the Results overview table, you can also navigate directly to the detailed results for a sample by

clicking the row of a sample of interest. For more information, see “View detailed results for a project”

on page 22.

1. To view the Results overview table, click the Results tab.

Note: The Results opens by default after an analysis is complete.

18 SeqScreener Gene Edit Conﬁrmation App User Guide

2. Customize the Results overview table or proceed to results details.

Option Description

Add project-speciﬁc notes Project notes are added to the exported analysis

results ﬁles (see “Export the Results overview

table” on page 29).

1. Click Add project notes , then enter

notes into the provided ﬁeld (see callout 3 in

Figure 2).

2. Click Save to save the notes to your project.

Note: You can edit project notes at any time by

clicking Add project notes , then editing the

text as needed.

Add sample-speciﬁc notes Sample notes are added to the exported analysis

results ﬁles (see “Export the Results overview

table” on page 29).

1. Click (Add sample notes) in the row of a

sample of interest, then enter notes into the

provided ﬁeld (see callout 5 in Figure 2).

2. Click Save to save the notes to your project.

A small notch in the grade column designates the

presence of notes for a sample (see callout 4 in

Figure 2).

Note: You can view or edit sample-speciﬁc notes

at any time by clicking (Add sample notes),

then editing the text as needed.

Sort the Results overview table Click the arrow in a header of a column to sort

the results according to the column category (see

callout 2 in Figure 2).

For example, click the arrow in the Editing (%)

column to view results from lowest to highest

editing percentage. Click the arrow again to

reverse the order.

Filter the Results overview table by plate If you imported more than one plate, you can sort

the Results overview table to display the results

for a speciﬁc plate.

Click (Filter) in the Plate column header,

then select a plate from the dropdown list to

display only the results for the selected plate (see

callout 1 in Figure 2). To view all plates, select

View all (default).

View detailed results for a sample Click within the row of a sample of interest.

Chapter 4 View results

View results summary 4

SeqScreener Gene Edit Conﬁrmation App User Guide 19

Option Description

The Details tab opens to the Overview screen,

with the sample of interest pre-selected on the

plate layout. For more information, see “View

detailed results for a project” on page 22.

2 3

Figure 2 Results tab

1Filter the table to display results for a speciﬁc plate or all

plates

2Sort the order in which results appear according to the

column category

3Add project-speciﬁc notes

4A notch designates the presence of sample-speciﬁc notes

5Add or edit sample-speciﬁc notes

6Export the Results overview table data

To export results, see “Export the Results overview table” on page 29.

How to ... Learn more about...

“Export the Results overview table” on page 29 “Results overview table” on page 20

“View past results” on page 28 “Editing grade categories” on page 27

“Results ﬁles” on page 31

Results overview table

The Results overview table contains the following information.

Column Description

Grade Each edited sample is assigned a grade that classiﬁes the gene editing

quality for that sample. For the list and description of each grade

category, see “Editing grade categories” on page 27.

Plate Plate name that was generated by the CE Sanger sequencing

instrument during data collection.

Chapter 4 View results

View results summary

20 SeqScreener Gene Edit Conﬁrmation App User Guide

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Thermo Fisher Scientific SeqScreener Gene Edit Confirmation App User guide

Brand: Thermo Fisher Scientific

Model: SeqScreener Gene Edit Confirmation App

Type: User guide

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Thermo Fisher Scientific SeqScreener Gene Edit Confirmation App User guide

Thermo Fisher Scientific SeqScreener Gene Edit Confirmation App User guide

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