READ ME File For 'Dataset supporting the University of Southampton Doctoral Thesis " Engineering glycosylation in HIV-1 vaccine design"'

Dataset DOI: https://doi.org/10.5258/SOTON/D2883

Date that the file was created: 12/2023

-------------------
GENERAL INFORMATION
-------------------

ReadMe Author: Alessio D'addabbo, University of Southampton 000-0003-2542-6465

Date of data collection: 2018/9/1 - 2023/7/19

Information about geographic location of data collection: Data collected in United Kingdom

Related projects:

This project has received funding from the European Union's Horizon 2020 Research and Innovation program under grant agreement no. 681137, the Bill and Melinda Gates Foundation through the Collaboration for AIDS Vaccine Discovery (OPP1084519 and OPP1115782)

--------------------------
SHARING/ACCESS INFORMATION
-------------------------- 

Licenses/restrictions placed on the data, or limitations of reuse: CC-BY

Recommended citation for the data:     
Dataset supporting the University of Southampton Doctoral Thesis " Engineering glycosylation in HIV-1 vaccine design"
D'Addabbo, A. (Creator), Seabright, G. E. (Contributor), Binley, J. M. (Contributor), Allen, J. (Contributor) & Crispin, M. (Supervisor), University of Southampton, 27 Nov 2023
Dataset

This dataset supports the publications:

AUTHORS:Gemma E.Seabright, Christopher A.Cottrell, Marit J.van Gils, Alessio D’addabbo,
David J.Harvey, Anna-Janina Behrens, Joel D.Allen, Yasunori Watanabe, Nicole
Scaringi Thomas, M. Polveroni, Allison Maker, Snezana Vasiljevic, Nataliade Val,
Rogier W.Sanders, Andrew B. Ward, Max Crispin
TITLE:Networks of HIV-1 Envelope Glycans Maintain Antibody Epitopes in the Face of Glycan Additions and Deletions
JOURNAL: Structure
PAPER DOI IF KNOWN: https://doi.org/10.1016/j.str.2020.04.022

AUTHORS:Emma T Crooks, Francisco Almanza, Alessio D’addabbo, Erika Duggan, Jinsong Zhang, Kshitij Wagh, Huihui Mou, Joel D Allen, Alyssa Thomas, Keiko Osawa, Bette T Korber, Yaroslav Tsybovsky, Evan Cale, John Nolan, Max Crispin, Laurent K Verkoczy, James M Binley
TITLE:Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine
regimens
JOURNAL: PLOS Pathogens
PAPER DOI IF KNOWN: https://doi.org/10.1371/journal.ppat.1009807

AUTHORS: Tommy Tong, Alessio D’Addabbo, Jiamin Xu, Himanshi Chawla, Albert Nguyen, Paola Ochoa, Max Crispin, James M. Binley
TITLE: Impact of stabilizing mutations on the antigenic profile and glycosylation of membrane-expressed HIV-1 envelope glycoprotein
JOURNAL: PLOS Pathogens
PAPER DOI IF KNOWN: https://doi.org/10.1371/journal.ppat.1011452

Links to other publicly accessible locations of the data:

Links/relationships to ancillary or related data sets: 


--------------------
DATA & FILE OVERVIEW
--------------------

This dataset contains:

[File list (filenames, directory structure (for zipped files) and brief description of all data files)]

Zipped folder containing excel files contianing data pertaining to chapters:
- Chapter 3 data.xlsx: All data associated with Chapter 3
- chapter 4 data.xlsx: All data associated with Chapter 4
- Chapter 5 data.xlsx: All data associated with Chapter 5
- Chapter 6 data.xlsx: All data associated with Chapter 6


Relationship between files, if important for context:  

Additional related data collected that was not included in the current data package:
Data in the chapters associated with above publications can be found on the journal websites

If data was derived from another source, list source:

If there are there multiple versions of the dataset, list the file updated, when and why update was made:
20/12/23 Update: Updated metadata, publications and DOI


--------------------------
METHODOLOGICAL INFORMATION
--------------------------

Precise methodological information can be found within the thesis methods section

Description of methods used for collection/generation of data: LC-MS using a Thermo Fisher Orbitrap Fusion or Orbitrap Eclipse instrument

Methods for processing the data: Protein Metrics Byos software

Software- or Instrument-specific information needed to interpret the data, including software and hardware version numbers: Data was interpreted using bespoke python code contained within thesis appendix

Standards and calibration information, if appropriate: n/a

Environmental/experimental conditions: n/a

Describe any quality-assurance procedures performed on the data: n/a

People involved with sample collection, processing, analysis and/or submission:
Joel Allen, Gemma Seabright, Himanshi Chawla, Max Crispin, James Binley


--------------------------
DATA-SPECIFIC INFORMATION <Create sections for each datafile or set, as appropriate>
--------------------------

Specific names of samples analysed in each chapter outlined at beginning of each chapter in thesis.

Chapter 3: 19 Samples analysed
Chapter 4: 10 Samples analysed
Chapter 5: 36 Samples analysed including replicates
Chapter 6: 24 Samples analysed including replicates