Get MC38B cell line RNA- and WEX-sequenced

[armish]

So that we can run @iskandr's pipeline on it and get a short-list of "neoepitopes" that we can work our way through.

Submitted MC38B cell pellets (as well as PBMCs from B6 mouse as our normal) to GeneWiz for RNA- and WEX-sequencing on 10/18. They will get back to us with the raw data by the end of November.

Here are the details for the sequencing:

[armish]

From GeneWiz (11/6):

Hi Bulent Arman,

An update for your current order is now available:

Service Line: Next Generation Sequencing
Order Type: Standard RNA-Seq
Order Number: 30-290309823
Order Name: MC38 Neoantigen (RNA)
PO Number: 379558
Project Status: Sample QC
Estimated Delivery Date: 11/27/2019 (barring any unexpected issues)

Please review the attached RNA concentrations from Qubit RNA assay and TapeStation report of your samples. Briefly, the total amount is enough to attempt library preparation with and the quality is good to work with. Library preparation will be arranged soon.

If there are any issues with your project or samples, we will reach out to you shortly.
You can check the status of your project in real time with the link below. Moreover, we will notify you again at the next status change.

https://clims4.genewiz.com/OrderSummary/Summary?OrderId=77bd899a-fa06-48cf-969f-100cdc75fd30&lobId=3&serviceId=3011

If applicable, associated data files with this project can be accessed at any time with the link below.

https://clims4.genewiz.com/OrderSummary/ViewResult?OrderId=77bd899a-fa06-48cf-969f-100cdc75fd30&lobId=3&serviceId=3011

Please do not hesitate to contact us with any questions.

Thank you for choosing GENEWIZ!

Sudi Chari, Ph. D.

Study Manager

Next Generation Sequencing
GENEWIZ LLC
111 Corporate Blvd.
South Plainfield, NJ 07080
+1-908-222-0711, ext. 1
+1-908-333-4511 (fax)
www.GENEWIZ.com
ngs@GENEWIZ.com
Specializing in Genomics Since 1999

Attachments:

• Uploading SampleQC-01-02-30-290309823-10312019.pdf…
• 2.NGS_SampleQC_Form-30-290309823_CustomerCopy.xlsx

Also from GeneWiz:

Hi Bulent Arman,

An update for your current order is now available:

Service Line: Next Generation Sequencing
Order Type: Exome Sequencing
Order Number: 30-290303045
Order Name: MC38 neoantigen project
PO Number: 379240
Project Status: Sample QC
Estimated Delivery Date: 11/27/2019 (barring any unexpected issues)

Please review the attached DNA concentrations from Qubit dsDNA assay and the gel picture of your samples. Briefly, the total amount is enough to attempt library preparation with and the quality is good to work with. Library preparation will be arranged soon.

If there are any issues with your project or samples, we will reach out to you shortly.
You can check the status of your project in real time with the link below. Moreover, we will notify you again at the next status change.

https://clims4.genewiz.com/OrderSummary/Summary?OrderId=3c5d89ac-42b6-4d80-a1e3-1bbe924533f1&lobId=3&serviceId=3023

If applicable, associated data files with this project can be accessed at any time with the link below.

https://clims4.genewiz.com/OrderSummary/ViewResult?OrderId=3c5d89ac-42b6-4d80-a1e3-1bbe924533f1&lobId=3&serviceId=3023

Please do not hesitate to contact us with any questions.

Thank you for choosing GENEWIZ!

Sudi Chari, Ph. D.

Study Manager

Next Generation Sequencing
GENEWIZ LLC
111 Corporate Blvd.
South Plainfield, NJ 07080
+1-908-222-0711, ext. 1
+1-908-333-4511 (fax)
www.GENEWIZ.com
ngs@GENEWIZ.com
Specializing in Genomics Since 1999

Attachment:
2.NGS_SampleQC_Form-30-290303045_CustomerCopy.xlsx

[armish]

From GeneWiz (11/11):

Hi Bulent Arman,

An update for your current order is now available:

Service Line: Next Generation Sequencing
Order Type: Exome Sequencing
Order Number: 30-290303045
Order Name: MC38 neoantigen project
PO Number: 379240
Project Status: Library Preparation, In Queue
Comments:
Estimated Delivery Date: 11/27/2019 (barring any unexpected issues)

If there are any issues with your project or samples, we will reach out to you shortly.
You can check the status of your project in real time with the link below. Moreover, we will notify you again at the next status change.

https://clims4.genewiz.com/OrderSummary/Summary?OrderId=3c5d89ac-42b6-4d80-a1e3-1bbe924533f1&lobId=3&serviceId=3023

If applicable, associated data files with this project can be accessed at any time with the link below.

https://clims4.genewiz.com/OrderSummary/ViewResult?OrderId=3c5d89ac-42b6-4d80-a1e3-1bbe924533f1&lobId=3&serviceId=3023

Please do not hesitate to contact us with any questions.

Thank you for choosing GENEWIZ!

Netha Ulahannan, PhD

Study Manager
Next Generation Sequencing
GENEWIZ LLC
111 Corporate Blvd.
South Plainfield, NJ 07080
+1-908-222-0711, ext. 1
+1-908-333-4511 (fax)
www.GENEWIZ.com
ngs@GENEWIZ.com
Specializing in Genomics Since 1999

[armish]

From GeneWiz (11/12):

From: "ngs@genewiz.com" ngs@genewiz.com
Date: Tuesday, November 12, 2019 at 10:04 AM
To: "Aksoy, Bulent" aksoyb@musc.edu
Cc: "yang.wang@genewiz.com" yang.wang@genewiz.com, "ngs@genewiz.com" ngs@genewiz.com
Subject: Update: GENEWIZ Project 30-290309823

CAUTION: External

Hi Bulent Arman,

An update for your current order is now available:

Service Line: Next Generation Sequencing
Order Type: Standard RNA-Seq
Order Number: 30-290309823
Order Name: MC38 Neoantigen (RNA)
PO Number: 379558
Project Status: Library Preparation, In Queue
Comments: Expected to start this week
Estimated Delivery Date: 11/27/2019 (barring any unexpected issues)

If there are any issues with your project or samples, we will reach out to you shortly.
You can check the status of your project in real time with the link below. Moreover, we will notify you again at the next status change.

https://clims4.genewiz.com/OrderSummary/Summary?OrderId=77bd899a-fa06-48cf-969f-100cdc75fd30&lobId=3&serviceId=3011

If applicable, associated data files with this project can be accessed at any time with the link below.

https://clims4.genewiz.com/OrderSummary/ViewResult?OrderId=77bd899a-fa06-48cf-969f-100cdc75fd30&lobId=3&serviceId=3011

Please do not hesitate to contact us with any questions.

Thank you for choosing GENEWIZ!

Netha Ulahannan, PhD

Study Manager

Next Generation Sequencing
GENEWIZ LLC
111 Corporate Blvd.
South Plainfield, NJ 07080
+1-908-222-0711, ext. 1
+1-908-333-4511 (fax)
www.GENEWIZ.com
ngs@GENEWIZ.com
Specializing in Genomics Since 1999

[armish]

From GeneWiz (11/12):

Hi Bulent Arman,

An update for your current order is now available:

Service Line: Next Generation Sequencing
Order Type: Exome Sequencing
Order Number: 30-290303045
Order Name: MC38 neoantigen project
PO Number: 379240
Project Status: Sequencing, In Queue
Comments:
Estimated Delivery Date: 11/27/2019 (barring any unexpected issues)

If there are any issues with your project or samples, we will reach out to you shortly.
You can check the status of your project in real time with the link below. Moreover, we will notify you again at the next status change.

https://clims4.genewiz.com/OrderSummary/Summary?OrderId=3c5d89ac-42b6-4d80-a1e3-1bbe924533f1&lobId=3&serviceId=3023

If applicable, associated data files with this project can be accessed at any time with the link below.

https://clims4.genewiz.com/OrderSummary/ViewResult?OrderId=3c5d89ac-42b6-4d80-a1e3-1bbe924533f1&lobId=3&serviceId=3023

Please do not hesitate to contact us with any questions.

Thank you for choosing GENEWIZ!

Netha Ulahannan, PhD

Study Manager
Next Generation Sequencing
GENEWIZ LLC
111 Corporate Blvd.
South Plainfield, NJ 07080
+1-908-222-0711, ext. 1
+1-908-333-4511 (fax)
www.GENEWIZ.com
ngs@GENEWIZ.com
Specializing in Genomics Since 1999

[armish]

From GeneWiz (11/19):

Hi Bulent Arman,

An update for your current order is now available:

Service Line: Next Generation Sequencing
Order Type: Standard RNA-Seq
Order Number: 30-290309823
Order Name: MC38 Neoantigen (RNA)
PO Number: 379558
Project Status: Library Preparation, Processing
Comments:
Estimated Delivery Date: 11/27/2019 (barring any unexpected issues)

If there are any issues with your project or samples, we will reach out to you shortly.
You can check the status of your project in real time with the link below. Moreover, we will notify you again at the next status change.

https://clims4.genewiz.com/OrderSummary/Summary?OrderId=77bd899a-fa06-48cf-969f-100cdc75fd30&lobId=3&serviceId=3011

If applicable, associated data files with this project can be accessed at any time with the link below.

https://clims4.genewiz.com/OrderSummary/ViewResult?OrderId=77bd899a-fa06-48cf-969f-100cdc75fd30&lobId=3&serviceId=3011

Please do not hesitate to contact us with any questions.

Thank you for choosing GENEWIZ!

Netha Ulahannan, PhD

Study Manager
Next Generation Sequencing
GENEWIZ LLC
111 Corporate Blvd.
South Plainfield, NJ 07080
+1-908-222-0711, ext. 1
+1-908-333-4511 (fax)
www.GENEWIZ.com
ngs@GENEWIZ.com
Specializing in Genomics Since 1999

[armish]

From GeneWiz (11/19):

Hi Bulent Arman,

An update for your current order is now available:

Service Line: Next Generation Sequencing
Order Type: Exome Sequencing
Order Number: 30-290303045
Order Name: MC38 neoantigen project
PO Number: 379240
Project Status: Sequencing, In Queue
Comments:
Estimated Delivery Date: 11/27/2019 (barring any unexpected issues)

If there are any issues with your project or samples, we will reach out to you shortly.
You can check the status of your project in real time with the link below. Moreover, we will notify you again at the next status change.

https://clims4.genewiz.com/OrderSummary/Summary?OrderId=3c5d89ac-42b6-4d80-a1e3-1bbe924533f1&lobId=3&serviceId=3023

If applicable, associated data files with this project can be accessed at any time with the link below.

https://clims4.genewiz.com/OrderSummary/ViewResult?OrderId=3c5d89ac-42b6-4d80-a1e3-1bbe924533f1&lobId=3&serviceId=3023

Please do not hesitate to contact us with any questions.

Thank you for choosing GENEWIZ!

Netha Ulahannan, PhD

Study Manager
Next Generation Sequencing
GENEWIZ LLC
111 Corporate Blvd.
South Plainfield, NJ 07080
+1-908-222-0711, ext. 1
+1-908-333-4511 (fax)
www.GENEWIZ.com
ngs@GENEWIZ.com
Specializing in Genomics Since 1999

[armish]

From GeneWiz (11/21):

Hi Bulent Arman,

An update for your current order is now available:

Service Line: Next Generation Sequencing
Order Type: Standard RNA-Seq
Order Number: 30-290309823
Order Name: MC38 Neoantigen (RNA)
PO Number: 379558
Project Status: Sequencing, In Queue
Comments:
Estimated Delivery Date: 11/27/2019 (barring any unexpected issues)

If there are any issues with your project or samples, we will reach out to you shortly.
You can check the status of your project in real time with the link below. Moreover, we will notify you again at the next status change.

https://clims4.genewiz.com/OrderSummary/Summary?OrderId=77bd899a-fa06-48cf-969f-100cdc75fd30&lobId=3&serviceId=3011

If applicable, associated data files with this project can be accessed at any time with the link below.

https://clims4.genewiz.com/OrderSummary/ViewResult?OrderId=77bd899a-fa06-48cf-969f-100cdc75fd30&lobId=3&serviceId=3011

Please do not hesitate to contact us with any questions.

Thank you for choosing GENEWIZ!

Netha Ulahannan, PhD

Study Manager
Next Generation Sequencing
GENEWIZ LLC
111 Corporate Blvd.
South Plainfield, NJ 07080
+1-908-222-0711, ext. 1
+1-908-333-4511 (fax)
www.GENEWIZ.com
ngs@GENEWIZ.com
Specializing in Genomics Since 1999

[armish]

The raw sequencing data sets have arrived and backed up on:

gs://musc-tcr-transfer/data/20191129-mc38-sequencing/:

gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290303045/:

gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290303045/00_fastq/:
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290303045/00_fastq/A-WES_R1_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290303045/00_fastq/A-WES_R2_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290303045/00_fastq/B-WES_R1_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290303045/00_fastq/B-WES_R2_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290303045/00_fastq/T-WES_R1_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290303045/00_fastq/T-WES_R2_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290303045/00_fastq/md5sum_list.txt

gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290309823/:

gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290309823/00_fastq/:
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290309823/00_fastq/A-RNA_R1_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290309823/00_fastq/A-RNA_R2_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290309823/00_fastq/B-RNA_R1_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290309823/00_fastq/B-RNA_R2_001.fastq.gz
gs://musc-tcr-transfer/data/20191129-mc38-sequencing/30-290309823/00_fastq/md5sum_list.txt

Will close this issue once I put the proper pointers up in the README file.

• A: MC38 (that we have been using for our other experiments so far)
• B: MC38B (from Aaron Ring; we used this for the actual tumor experiments so TCRs should be specific to this)
• T: bulk T cells from B6 mice (this is the mouse we injected MC38B subcatenously)