4 research outputs found
Additional file 2: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues
- Author
- Agata Wesolowska-Andersen (3683038)
- Andrew Smith (11197)
- Celeste Eng (179050)
- Cydney Rios (3683041)
- Eleazar Eskin (108069)
- Erez Levanon (3408371)
- Esteban Burchard (1262)
- Franziska Gruhl (220206)
- Hagit Porath (4485907)
- Harry Yang (4376224)
- Jose Santana (421066)
- Kevin Hsieh (4973062)
- Linus Chen (4973059)
- Max Seibold (3683044)
- Nicolas Strauli (3551255)
- Noah Zaitlen (120787)
- Prescott Woodruff (4055044)
- Roberto Spreafico (4246897)
- Roel Ophoff (573364)
- Ryan Hernandez (218444)
- Sagiv Shifman (86805)
- Serghei Mangul (4973068)
- Stephanie Christenson (4973065)
- Timothy Daley (3312627)
- Publication venue
- Publication date
- Field of study
Table S1. The effect of altering order of ROP step on the classification accuracy. Table S2. Concordance of targeted TCRB-Seq and ROP based on three TCGA samples from kidney renal clear cell carcinoma (KIRC). Table S4. RNA-seq datasets overview. Table S5. Genomic profile of unmapped reads reported for each dataset (S1, S2, S3). Table S6. Relative genomic abundance of microbial taxa at different levels of taxonomic classification after removal of reads with human origin (average over all samples of three tissues, performed for in-house RNA-Seqdata). Table S7. Genomic profile of unmapped reads across two SRA RNA-seq samples using ROP v1.0.8. Percentage for each category is calculated as a fraction from the total number of reads. (PDF 100 kb
Additional file 1: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues
- Author
- Agata Wesolowska-Andersen (3683038)
- Andrew Smith (11197)
- Celeste Eng (179050)
- Cydney Rios (3683041)
- Eleazar Eskin (108069)
- Erez Levanon (3408371)
- Esteban Burchard (1262)
- Franziska Gruhl (220206)
- Hagit Porath (4485907)
- Harry Yang (4376224)
- Jose Santana (421066)
- Kevin Hsieh (4973062)
- Linus Chen (4973059)
- Max Seibold (3683044)
- Nicolas Strauli (3551255)
- Noah Zaitlen (120787)
- Prescott Woodruff (4055044)
- Roberto Spreafico (4246897)
- Roel Ophoff (573364)
- Ryan Hernandez (218444)
- Sagiv Shifman (86805)
- Serghei Mangul (4973068)
- Stephanie Christenson (4973065)
- Timothy Daley (3312627)
- Publication venue
- Publication date
- Field of study
Supplementary methods. (PDF 789 kb
Additional file 3: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues
- Author
- Agata Wesolowska-Andersen (3683038)
- Andrew Smith (11197)
- Celeste Eng (179050)
- Cydney Rios (3683041)
- Eleazar Eskin (108069)
- Erez Levanon (3408371)
- Esteban Burchard (1262)
- Franziska Gruhl (220206)
- Hagit Porath (4485907)
- Harry Yang (4376224)
- Jose Santana (421066)
- Kevin Hsieh (4973062)
- Linus Chen (4973059)
- Max Seibold (3683044)
- Nicolas Strauli (3551255)
- Noah Zaitlen (120787)
- Prescott Woodruff (4055044)
- Roberto Spreafico (4246897)
- Roel Ophoff (573364)
- Ryan Hernandez (218444)
- Sagiv Shifman (86805)
- Serghei Mangul (4973068)
- Stephanie Christenson (4973065)
- Timothy Daley (3312627)
- Publication venue
- Publication date
- Field of study
Table S3. The list of the 2000 SRA RNA-seq samples used in the analysis. SRA samples were randomly selected from the Sequence Read Archive (SRA). (CSV 22 kb
COVID-19 Host Genetics Initiative. A first update on mapping the human genetic architecture of COVID-19
- Author
- A Cerny (13566592)
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- Matteo Della Monica (13566748)
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- Rasoul Aliannejad (10054106)
- Ravaglia Sabrina (13566802)
- Raymond Chung (1955386)
- Raymond K Walters (13566184)
- Reedik Magi (61757)
- Renato Polimanti (3043917)
- Renzo Scaggiante (6104627)
- Riccardo Colombo (94203)
- Richard C Trembath (9257558)
- Richard H Scott (13567189)
- Richard J Packer (11075223)
- Rita Perna (13566829)
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- Robert C Free (8880545)
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- Robert P Sebra (13567000)
- Robert Warmerdam (13566973)
- Roberta Russo (587655)
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- Roger Colobran (824193)
- Ron Do (201540)
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- Rui Li (4631)
- Ruth JF Loos (3810124)
- Ryan C Thompson (13566994)
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- Sabine Claassen (13566256)
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- Saeideh Ahmadi (13566940)
- Salam Massadeh (6628496)
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- Sam Choi (1977952)
- Sameer Chavan (3947117)
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- Sami Koskelainen (13566451)
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- Samuli Ripatti (144251)
- Sandra P Smieszek (13567231)
- Sandro Mancarella (9467152)
- Sandro Panese (6444245)
- Sang Hyuck Lee (13566892)
- Sanni Ruotsalainen (13566448)
- Sara Alotaibi (13567108)
- Sara Amitrano (9656605)
- Sara Pigazzini (13566247)
- Sarah Alkwai (13567126)
- Sarah Finer (237152)
- Sarah G Earle (13567204)
- Sauro Luchi (13566805)
- Saverio Giuseppe Parisi (4026326)
- Scott T Weiss (9407556)
- Sebastian Garcia-Madrona (13567324)
- Sebastian Zollner (13566925)
- Semira Gonseth Nussle (13566460)
- Serafina Valente (3753733)
- Serena Ludovisi (13566814)
- Serghei Mangul (4973068)
- Sergio Daga (11283239)
- Seyed Behrooz Mohseni Moghaddam (13566943)
- Shaheen Akhtar (192582)
- Shang-Kuan Lin (13567207)
- Shannon McCurdy (11944312)
- Shapna Hussain (13566886)
- Shawn N Murphy (4802670)
- Shawneequa Callier (13567228)
- Shea J Andrews (13566199)
- Shefa Miah (13566901)
- Shefali S Verma (13567090)
- Shona M Kerr (8950520)
- Silvia Baroni (2156290)
- Silvia Cappelli (13566712)
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- Simona Dei (13566808)
- Simona Marcantonio (9656611)
- Simona Sarzi-Braga (13566784)
- Simone Furini (173392)
- Slayton J Underwood (13566208)
- Sophie Venturelli (9326809)
- Souad Rahmouni (320501)
- Spencer Knight (13566223)
- Stefania Mantovani (202342)
- Stefano Baratti (13566817)
- Stefano Busani (735718)
- Stefano Ceri (3614225)
- Stefano Rusconi (237803)
- Stephanie Bibert (316131)
- Stephanie Gofflot (790863)
- Stephen J Wicks (13566349)
- Steven Ascolillo (13566991)
- Stuart C Sealfon (13566205)
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- Susan Walker (469919)
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- Tim D Spector (8543481)
- Tiziana Bachetti (361249)
- Tom Fowler (3624713)
- Tomas Segura (13567309)
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- Tomoko Nakanishi (344291)
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- Tooraj Mirshahi (547507)
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- Triin Laisk (6103775)
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- V D'Acremont (13566580)
- V Eric Kerchberger (13566334)
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- Valentina Anemoli (13566724)
- Vasilios Polymeropoulos (13567237)
- Veronica Rico (13567261)
- Veronica Robles (7338719)
- Veronique Erard (13566466)
- Victor Moreno (748751)
- Vijay G Sankaran (13566175)
- Vincent Mooser (47546)
- Vincenzo Forgetta (756326)
- Voraphoj Nilaratanakul (13566964)
- Vorasuk Shotelersuk (581000)
- Walaa A Felemban (13567150)
- Walaa M El-Lawaty (13566397)
- Walid T Khafaga (13566394)
- Wanna Chetruengchai (9659225)
- Wanying Zhu (1567963)
- Watsamon Jantarabenjakul (9504660)
- WC Albrich (13566586)
- Wei Zhou (24328)
- Wenhan Lu (8908976)
- Werner Albrich (5541584)
- Xavier Farre (10317580)
- Xiao Chang (43560)
- Xiaoqing Xue (6116318)
- Xueyang Wang (6813818)
- Y Lannepoudenx (13566508)
- Yan Sun (22436)
- Yaseen M Arabi (12041017)
- Yasmine Belhaj (13566250)
- Yasser M El-Sherbiny (13566358)
- Yen-Chen Anne Feng (9983636)
- Yuk-Lam Ho (7010873)
- Yuki Bradford (496693)
- Yunsung Lee (10670517)
- Yuval Itan (260527)
- Yves Beguin (264097)
- Zaman Afrasiabi (10905751)
- Zeinab Naderpour (10054118)
- Ziab Z Alahmadey (13567144)
- Publication venue
- Publication date
- 03/08/2022
- Field of study
The COVID-19 pandemic continues to pose a major public health threat, especially in countries with low vaccination rates. To better understand the biological underpinnings of SARS-CoV-2 infection and COVID-19 severity, we formed the COVID-19 Host Genetics Initiative1. Here we present a genome-wide association study meta-analysis of up to 125,584 cases and over 2.5 million control individuals across 60 studies from 25 countries, adding 11 genome-wide significant loci compared with those previously identified2. Genes at new loci, including SFTPD, MUC5B and ACE2, reveal compelling insights regarding disease susceptibility and severity.</p