C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING最新文献

{"title":"Non-Fibrotic Central Lung Gene Expressions Associate with Myofibroblasts Activity in Idiopathic Pulmonary Fibrosis","authors":"Y. Huang, R. Guzy, S. Ma, J. Kim, C. Bonham, C. Hogaboam, A. Sperling, I. Noth","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4988","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4988","url":null,"abstract":"","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134325156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interactive Web-Based Lung Cell Atlases Lower Barriers to Transcriptomic Data Sharing, Mining and Dissemination","authors":"C. Cosme Jr, J. Flint, N. Neumark, N. Kothapalli, A. Balayev, T. Adams, J. Schupp, J. Mcdonough, X. Yan, M. Sauler, N. Kaminski","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4978","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4978","url":null,"abstract":"Rationale: Recent advancements in sequencing technologies have led to a substantial increase in the scale and resolution of transcriptomic data. Despite this progress, accessibility to this data, particularly among those who are coming from non-computational backgrounds is limited. To facilitate improved access and exploration of our single-cell RNA sequencing data, we generated several data sharing, mining and dissemination portals to accompany our idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), and lung endothelial cells (Lung EC) cell atlases. Descriptions and links of each website can be found here: https://medicine.yale.edu/lab/kaminski/research/atlas/. Methods: Each interactive data mining website is coded in the R language using the Shiny package and is hosted by Shinyapps.io. Percell expression data for each website is stored on a MySQL database hosted by Amazon Web Services (AWS). Time-associated website engagement statistics and gene query information is collected for each website using a combination of Google Analytics and a gene search table stored on our MySQL database. User exploration of available data is facilitated through several easy-touse visualization tools available on each website. Results: Website usage statistics since the publication of each website shows that 9,772 unique users from 56 countries and five continents have accessed at least one of the three websites. At the time of writing, 300,748 total queries have been made for 15,627 unique genes across the websites. The top five searched genes for the IPF Cell Atlas are CD14, ACE2, ACTA2, IL11 and MUC5B while for the COPD Cell Atlas they are FAM13A, MIRLET7BHG, HHIP, ISM1 and DDT. Finally, the top searched genes for the Lung Endothelial Cell Atlas are BMPR2, PECAM1, EDNRB, APLNR and PROX1. Of note, interaction with the IPF Cell Atlas increased dramatically at the start of the COVID-19 pandemic, with queries for the ACE2 gene, the putative binding receptor for the SARS-CoV-2 virus, increasing substantially at the pandemic's onset in the United States. Conclusions: Usage statistics, gene query information and feedback from users, both within academia and industry, have shown broad engagement with our websites by individuals across computational and non-computational backgrounds. We envision widespread adoption of web-based portals similar to ours will facilitate novel discoveries within these complex datasets and new scientific collaborations.","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130957083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Basal-Like Cells Cultured from Peripheral Fibrotic Lung Tissue Show Transcriptomic Differences to Airway Basal Cells","authors":"P. Khan, S. Blumer, J. Roux, S. Savic, L. Knudsen, D. Jonigk, M. Kuehnel, M. Tamm, K. Hostettler","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4993","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4993","url":null,"abstract":"","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"553 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115732754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Idiopathic Pulmonary Fibrosis-Associated SNP rs35705950 Is Transcribed in a MUC5B Promoter Associated Long Non-Coding RNA (AC061979.1)","authors":"I. Enekwa, R. Neatu, G. Fois, M. Frick, S. Moschos","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4974","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4974","url":null,"abstract":"","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"133 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132802187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LungGENIE: The Lung Gene Expression and Network Imputation Engine","authors":"A. Ghosh, J. Hess, C. Hersh, S. Glatt","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4984","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4984","url":null,"abstract":"","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129229899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MUC5B Is an Endotype-Dependent Expression Quantitative Trait Locus in Idiopathic Pulmonary Fibrosis","authors":"A. Ghosh, M. Moll, B. Hobbs, W. Kim, P. Castaldi, E. Silverman, M. Cho, I. Yang, C. Hersh","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4973","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4973","url":null,"abstract":"","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"96 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116303054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiomic Sequencing Implicates TWIST1 as a Key Positive Regulator in Idiopathic Pulmonary Fibrosis Myofibroblast Differentiation","authors":"E. Valenzi, H. Bahudhanapati, T. Tabib, J. Tan, J. Sembrat, D. Kass, R. Lafyatis","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4987","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4987","url":null,"abstract":"","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116336847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lung Transplantation for Idiopathic Pulmonary Fibrosis Enriches for Individuals with Telomere-Mediated Disease","authors":"J. Alder, R. Sutton, C. Iasella, S. Nouraie, R. Koshy, S. Hannan, E. Chan, X. Chen, Y. Zhang, M. Brown, I. Popescu, M. Veatch, S. Saul, A. Berndt, B. Methé, A. Morris, J. Pilewski, P. Sanchez, M. Morrell, S. Shapiro, K. Lindell, K. Gibson, D. Kass, J. McDyer","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4976","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4976","url":null,"abstract":"","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"97 ","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120970939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deconvolution of Spatial Transcriptomic Allows to Predict the Spatial Location of Each Cell Type of Interest in the Fibrotic Lung","authors":"A. Justet, T. Adams, A. Balayev, T. Bärnthaler, C. Cosme Jr, J. Mcdonough, J. Flint, J. Schupp, A. Zhao, J. Deluliis, F. Ahangari, X. Yan, N. Kaminski","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4991","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4991","url":null,"abstract":"","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"143 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127505588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential IPF Associated Gene Expression and DNA Methylation Changes in Human Airway and Parenchymal Fibroblasts","authors":"P. Rajasekar, A. Lagan, J. Patel, B. Barksby, R. Burgoyne, J. MacIsaac, D. Lin, S.T. May, M. Castellanos-Uribe, M. Kobor, T. Hackett, A. Halayko, A. Knox, A. Fisher, L. Borthwick, R. Clifford","doi":"10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4977","DOIUrl":"https://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4977","url":null,"abstract":"","PeriodicalId":382658,"journal":{"name":"C109. PULMONARY FIBROSIS: MOVING FORWARD WITH GENETICS AND SEQUENCING","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132340011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}