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hammerlab / tcr-transfer

Explore an alternative way to clone TILs by first single-cell TCR-seq'ing them and then transforming non-exhausted T cells with these TIL TCRs
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Get MC38B cell line RNA- and WEX-sequenced #5

Closed armish closed 3 years ago

armish commented 4 years ago

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:

Image 2019-10-18 at 2 29 02 PM Image 2019-10-18 at 2 30 26 PM
armish commented 4 years ago

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:

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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.