--- a/README.md
+++ b/README.md
@@ -1,63 +1,63 @@
-# COVIDPBMC
-### Multi-omics profiling of peripheral immune system response to SARS-CoV-2 infection.
-
-The COVID-19 pandemic, caused by SARS coronavirus 2 (SARS-CoV-2), has resulted in excess morbidity and mortality as well as economic decline. To characterise the systemic host immune response to SARS-CoV-2, we performed single-cell RNA-sequencing coupled with analysis of cell surface proteins and T and B lymphocyte antigen receptor repertoires, providing molecular profiling of over 800,000 peripheral blood mononuclear cells from a cohort of 130 patients with COVID-19.  Our cohort, from three UK centres, spans the spectrum of clinical presentations and disease severities ranging from asymptomatic to critical.
-
-For more information, please read our manuscript published in [***Nature Medicine***](https://www.nature.com/articles/s41591-021-01329-2):
-
-*Emily Stephenson, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B Worlock, Masahiro Yoshida, Natsuhiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K Wilson, Nicole Mende, Laura Jardine, Louis CS Gardner, Issac Goh, Dave Horsfall, Jim McGrath, Simone Webb, Michael W Mather, Rik GH Lindeboom, Emma Dann, Ni Huang, Krzysztof Polanski, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P Payne, Kenneth F Baker, Aidan T Hanrath, Ina CD Schim van der Loeff, Andrew S Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Federica Mescia, Josephine L Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Sam M Janes, Claire M Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M Coxhead, Vladimir Y Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W King, Anthony J Rostron, A John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A Lyons, Kerstin B Meyer, Marko Z Nikolic, Christopher JA Duncan, Ken Smith, Sarah A Teichmann, Menna R Clatworthy, John C Marioni, Berthold Gottgens, Muzlifah Haniffa.* ***Single-cell multi-omics analysis of the immune response in COVID-19***. *Nature Medicine 2021.04.20; doi: https://dx.doi.org/10.1038/s41591-021-01329-2*
-
-
-Original preprint:
-
-*Emily Stephenson, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B Worlock, Masahiro Yoshida, Natsuhiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K Wilson, Nicole Mende, Laura Jardine, Louis CS Gardner, Issac Goh, Dave Horsfall, Jim McGrath, Simone Webb, Michael W Mather, Rik GH Lindeboom, Emma Dann, Ni Huang, Krzysztof Polanski, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P Payne, Kenneth F Baker, Aidan T Hanrath, Ina CD Schim van der Loeff, Andrew S Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Federica Mescia, Josephine L Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Sam M Janes, Claire M Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M Coxhead, Vladimir Y Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W King, Anthony J Rostron, A John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A Lyons, Kerstin B Meyer, Marko Z Nikolic, Christopher JA Duncan, Ken Smith, Sarah A Teichmann, Menna R Clatworthy, John C Marioni, Berthold Gottgens, Muzlifah Haniffa.* ***The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres***. *medRxiv 2021.01.13.21249725; doi: https://doi.org/10.1101/2021.01.13.21249725*
-
-
-## Web portal
-<a href="https://www.sanger.ac.uk/" rel="Wellcome Trust Sanger Institute"><img src="https://www.covid19cellatlas.org/logos/sanger.png" height="100"></a>
-<a href="https://data.humancellatlas.org/" rel="Human cell atlas"><img src="https://www.covid19cellatlas.org/logos/human-cell-atlas.png" height="100"></a>
-<a href="https://chanzuckerberg.com/" rel="Chan-Zuckerberg Initiative"><img src="https://www.covid19cellatlas.org/logos/chan-zuckerberg-initiative.png" height="100"></a>
-
-Explore the full COVID-19 cell atlas [here](https://www.covid19cellatlas.org/).
-
-Data is available under `COVID-19 PBMC Ncl-Cambridge-UCL`. Interactive view available [here](https://covid19cellatlas.org/haniffa21).
-
-
-## Research Groups
-<a href="https://haniffalab.com" rel="Haniffa Lab"><img src="https://avatars0.githubusercontent.com/u/44367631?s=200&v=4" height="100"></a>
-
-[Haniffa Lab github](https://github.com/haniffalab) [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/haniffalab.svg?style=social&label=Follow%20%40haniffalab)](https://twitter.com/haniffalab)
-
-<a href="https://www.teichlab.org" rel="Teichmann Lab"><img src="http://static1.squarespace.com/static/56d85b53c6fc08fe12541664/t/580e213129687fbc612f9a5c/1610115725446/?format=1500w" height="100"></a>
-
-[Teichmann Lab github](https://github.com/Teichlab) [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/teichlab.svg?style=social&label=Follow%20%40teichlab)](https://twitter.com/teichlab)
-
-<a href="https://github.com/MarioniLab" rel="Marioni Lab"><img src="https://avatars3.githubusercontent.com/u/16623186?s=200&v=4" height="100"></a>
-
-[Marioni Lab github](https://github.com/MarioniLab) [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/marionilab.svg?style=social&label=Follow%20%40marionilab)](https://twitter.com/marionilab)
-
-[Göttgens Lab](http://www.haem.cam.ac.uk/staff/senior-staff/professor-bertie-gottgens/)
-
-<a href="https://clatworthylab.github.io/" rel="Clatworthy Lab"><img src="https://clatworthylab.github.io/assets/img/clatworthylab_bold.svg" height="100"></a> [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/clatworthylab.svg?style=social&label=Follow%20%40clatworthylab)](https://twitter.com/clatworthylab)
-
-[Clatworthy Lab](https://www.med.cam.ac.uk/clatworthy/)
-
-
-
-## BCR analysis package
-<a href="https://sc-dandelion.readthedocs.io/" rel="dandelion"><img src="https://github.com/zktuong/dandelion/blob/master/docs/notebooks/img/dandelion_logo.png" height="100"></a>
-
-[dandelion github](https://github.com/zktuong/dandelion)
-
-BCR AIRR files are available [here](https://github.com/clatworthylab/COVID_analysis).
-
-## Contacts
-Please email the corresponding authors in the main manuscript for other requests (https://www.nature.com/articles/s41591-021-01329-2).
-
-For specific queries related to this repository, please contact one of the following:
-
-https://github.com/MikeDMorgan [![Twitter URL](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/MDMorgan_cam)
-
-https://github.com/greynolds81 [![Twitter URL](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/gary_d_reynolds)
-
-https://github.com/zktuong [![Twitter URL](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/KelvinTuong)
+# COVIDPBMC
+### Multi-omics profiling of peripheral immune system response to SARS-CoV-2 infection.
+
+The COVID-19 pandemic, caused by SARS coronavirus 2 (SARS-CoV-2), has resulted in excess morbidity and mortality as well as economic decline. To characterise the systemic host immune response to SARS-CoV-2, we performed single-cell RNA-sequencing coupled with analysis of cell surface proteins and T and B lymphocyte antigen receptor repertoires, providing molecular profiling of over 800,000 peripheral blood mononuclear cells from a cohort of 130 patients with COVID-19.  Our cohort, from three UK centres, spans the spectrum of clinical presentations and disease severities ranging from asymptomatic to critical.
+
+For more information, please read our manuscript published in [***Nature Medicine***](https://www.nature.com/articles/s41591-021-01329-2):
+
+*Emily Stephenson, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B Worlock, Masahiro Yoshida, Natsuhiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K Wilson, Nicole Mende, Laura Jardine, Louis CS Gardner, Issac Goh, Dave Horsfall, Jim McGrath, Simone Webb, Michael W Mather, Rik GH Lindeboom, Emma Dann, Ni Huang, Krzysztof Polanski, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P Payne, Kenneth F Baker, Aidan T Hanrath, Ina CD Schim van der Loeff, Andrew S Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Federica Mescia, Josephine L Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Sam M Janes, Claire M Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M Coxhead, Vladimir Y Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W King, Anthony J Rostron, A John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A Lyons, Kerstin B Meyer, Marko Z Nikolic, Christopher JA Duncan, Ken Smith, Sarah A Teichmann, Menna R Clatworthy, John C Marioni, Berthold Gottgens, Muzlifah Haniffa.* ***Single-cell multi-omics analysis of the immune response in COVID-19***. *Nature Medicine 2021.04.20; doi: https://dx.doi.org/10.1038/s41591-021-01329-2*
+
+
+Original preprint:
+
+*Emily Stephenson, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B Worlock, Masahiro Yoshida, Natsuhiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K Wilson, Nicole Mende, Laura Jardine, Louis CS Gardner, Issac Goh, Dave Horsfall, Jim McGrath, Simone Webb, Michael W Mather, Rik GH Lindeboom, Emma Dann, Ni Huang, Krzysztof Polanski, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P Payne, Kenneth F Baker, Aidan T Hanrath, Ina CD Schim van der Loeff, Andrew S Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Federica Mescia, Josephine L Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Sam M Janes, Claire M Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M Coxhead, Vladimir Y Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W King, Anthony J Rostron, A John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A Lyons, Kerstin B Meyer, Marko Z Nikolic, Christopher JA Duncan, Ken Smith, Sarah A Teichmann, Menna R Clatworthy, John C Marioni, Berthold Gottgens, Muzlifah Haniffa.* ***The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres***. *medRxiv 2021.01.13.21249725; doi: https://doi.org/10.1101/2021.01.13.21249725*
+
+
+## Web portal
+<a href="https://www.sanger.ac.uk/" rel="Wellcome Trust Sanger Institute"><img src="https://www.covid19cellatlas.org/logos/sanger.png" height="100"></a>
+<a href="https://data.humancellatlas.org/" rel="Human cell atlas"><img src="https://www.covid19cellatlas.org/logos/human-cell-atlas.png" height="100"></a>
+<a href="https://chanzuckerberg.com/" rel="Chan-Zuckerberg Initiative"><img src="https://www.covid19cellatlas.org/logos/chan-zuckerberg-initiative.png" height="100"></a>
+
+Explore the full COVID-19 cell atlas [here](https://www.covid19cellatlas.org/).
+
+Data is available under `COVID-19 PBMC Ncl-Cambridge-UCL`. Interactive view available [here](https://covid19cellatlas.org/haniffa21).
+
+
+## Research Groups
+<a href="https://haniffalab.com" rel="Haniffa Lab"><img src="https://avatars0.githubusercontent.com/u/44367631?s=200&v=4" height="100"></a>
+
+[Haniffa Lab github](https://github.com/haniffalab) [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/haniffalab.svg?style=social&label=Follow%20%40haniffalab)](https://twitter.com/haniffalab)
+
+<a href="https://www.teichlab.org" rel="Teichmann Lab"><img src="http://static1.squarespace.com/static/56d85b53c6fc08fe12541664/t/580e213129687fbc612f9a5c/1610115725446/?format=1500w" height="100"></a>
+
+[Teichmann Lab github](https://github.com/Teichlab) [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/teichlab.svg?style=social&label=Follow%20%40teichlab)](https://twitter.com/teichlab)
+
+<a href="https://github.com/MarioniLab" rel="Marioni Lab"><img src="https://avatars3.githubusercontent.com/u/16623186?s=200&v=4" height="100"></a>
+
+[Marioni Lab github](https://github.com/MarioniLab) [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/marionilab.svg?style=social&label=Follow%20%40marionilab)](https://twitter.com/marionilab)
+
+[Göttgens Lab](http://www.haem.cam.ac.uk/staff/senior-staff/professor-bertie-gottgens/)
+
+<a href="https://clatworthylab.github.io/" rel="Clatworthy Lab"><img src="https://clatworthylab.github.io/assets/img/clatworthylab_bold.svg" height="100"></a> [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/clatworthylab.svg?style=social&label=Follow%20%40clatworthylab)](https://twitter.com/clatworthylab)
+
+[Clatworthy Lab](https://www.med.cam.ac.uk/clatworthy/)
+
+
+
+## BCR analysis package
+<a href="https://sc-dandelion.readthedocs.io/" rel="dandelion"><img src="https://github.com/zktuong/dandelion/blob/master/docs/notebooks/img/dandelion_logo.png?raw=true" height="100"></a>
+
+[dandelion github](https://github.com/zktuong/dandelion)
+
+BCR AIRR files are available [here](https://github.com/clatworthylab/COVID_analysis).
+
+## Contacts
+Please email the corresponding authors in the main manuscript for other requests (https://www.nature.com/articles/s41591-021-01329-2).
+
+For specific queries related to this repository, please contact one of the following:
+
+https://github.com/MikeDMorgan [![Twitter URL](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/MDMorgan_cam)
+
+https://github.com/greynolds81 [![Twitter URL](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/gary_d_reynolds)
+
+https://github.com/zktuong [![Twitter URL](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/KelvinTuong)