Mtb specific HLA-E restricted CD8+ TCRs

[lvoogdLUMC]

VDJ sequences of Mtb peptide specific CD8+ TCRs recognizing two HLA-E specific Mtb peptides that have been identified via tetramer sorting and sequencing.

Belongs to the manuscript: Mtb specific HLA-E restricted CD8+ T-cells have a highly diverse TCR repertoire (paper pending).

VDJ and CDR3_VDJDB-database.xlsx

[mikessh]

Hello @lvoogdLUMC, It seems that you have not attached the sequences. If you need assistance with formatting the data let me know

[lvoogdLUMC]

Hello,

That’s true. We are currently putting the data together as I forgot some sequences and I will upload these when I am back in the office on June 19.

All the best, Linda

Op 1 jun. 2023 om 05:05 heeft Mikhail Shugay @.***> het volgende geschreven:



Hello @lvoogdLUMChttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FlvoogdLUMC&data=05%7C01%7Cl.voogd%40lumc.nl%7C16e9d14f9666455cfb6608db624d151a%7Cc4048c4fdd544cbd80495457aacd2fb8%7C0%7C0%7C638211855433363641%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mN9kETNR6I4w4ueN766XS5k1IHLJEYC7vv1LpEQAlGg%3D&reserved=0, It seems that you have not attached the sequences. If you need assistance with formatting the data let me know

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fantigenomics%2Fvdjdb-db%2Fissues%2F351%23issuecomment-1571260539&data=05%7C01%7Cl.voogd%40lumc.nl%7C16e9d14f9666455cfb6608db624d151a%7Cc4048c4fdd544cbd80495457aacd2fb8%7C0%7C0%7C638211855433363641%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PYhnV4NRGZBVxvs8Gu45MTe%2B4q9YpvM7qSFbkT8DjW0%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FBACKTJH26ES7XTAQUK6SY2DXJABIHANCNFSM6AAAAAAYNPPG5Y&data=05%7C01%7Cl.voogd%40lumc.nl%7C16e9d14f9666455cfb6608db624d151a%7Cc4048c4fdd544cbd80495457aacd2fb8%7C0%7C0%7C638211855433363641%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=KJULSqiy6SNYQ8d6IXDkJSzzQ2J2%2F86Tp2J8yPlysBE%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

[lvoogdLUMC]

Hello @lvoogdLUMC, It seems that you have not attached the sequences. If you need assistance with formatting the data let me know

@mikessh I have attached an Excel file with the TCR sequences. Could you let me know if the format is ok?

Best, Linda Voogd

[mikessh]

Perhaps you can reformat it for this template https://raw.githubusercontent.com/antigenomics/vdjdb-db/master/template.xls ? It miss cell counts for each alpha/beta variant (those are not paired-chain, right?). And can you also please provide me the reference to the paper (doi or pubmed id). If it is unpublished I'll just make reference to this issue and fix it later.

[lvoogdLUMC]

@mikessh I have adjusted the file according to your template, thanks. These alpha/beta chains that are next to each other in the excel file are paired (per chunk.id). The paper is not yet published, which will hopefully happen soon. VDJ and CDR3_submission.xlsx

[mikessh]

@lvoogdLUMC hello, any news on the Pubmed ID of the paper?

[lvoogdLUMC]

@mikessh hello, no we are in the submission process and are waiting for reply of the editor. Publication might take a several weeks from now.

[lvoogdLUMC]

@mikessh Dear Mike, the paper is now published in iScience: Voogd et al., iScience 27, https://doi.org/10.1016/j.isci.2024.109233

Could you please add this reference to the data file with TCR sequences?

Thank you