DOI: 10.5281/zenodo.4757764
title: Preprocessing of Public RNA-sequencing Datasets to Facilitate Downstream Analyses of Human Diseases: Dataset

description: <strong>Publicly available RNA-sequencing (RNA-seq) data are a rich resource for elucidating the mechanisms of human disease; however, preprocessing these data requires considerable bioinformatic expertise and computational infrastructure. Analyzing multiple datasets with a consistent computational workflow increases the accuracy of downstream meta-analyses. This collection of datasets represents the human intracellular transcriptional response to disorders and diseases such as acute lymphoblastic leukemia (ALL), B-cell lymphomas, chronic obstructive pulmonary disease (COPD), colorectal cancer, lupus erythematosus; as well as infection with pathogens including Borrelia burgdorferi, hantavirus, influenza A virus, Middle East respiratory syndrome coronavirus (MERS-CoV), Streptococcus pneumoniae, respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We calculated the statistically significant differentially expressed genes and Gene Ontology (GO) terms for all datasets. In addition, a subset of the datasets also include results from splice variant analyses, intracellular signaling pathway enrichments as well as read mapping and quantification. All analyses were performed using well-established algorithms and are provided to facilitate future data mining activities, wet lab studies, and to accelerate collaboration and discovery.</strong>
description: {"references": ["Pullarkat VA, Lacayo NJ, Jabbour E, Rubnitz JE, Bajel A, Laetsch TW, Leonard J, Colace SI, Khaw SL, Fleming SA, Mattison RJ, Norris R, Opferman JT, Roberts KG, Zhao Y, Qu C, Badawi M, Schmidt M, Tong B, Pesko JC, Sun Y, Ross JA, Vishwamitra D, Rosenwinkel L, Kim SY, Jacobson A, Mullighan CG, Alexander TB, Stock W. 2021. Venetoclax and Navitoclax in Combination with Chemotherapy in Patients with Relapsed or Refractory Acute Lymphoblastic Leukemia and Lymphoblastic Lymphoma. Cancer Discov https://doi.org/10.1158/2159-8290.CD-20-1465.", "Faramand R, Jain M, Staedtke V, Kotani H, Bai R, Reid K, Lee SB, Spitler K, Wang X, Cao B, Pinilla J, Lazaryan A, Khimani F, Shah B, Chavez JC, Nishihori T, Mishra A, Mullinax J, Gonzalez R, Hussaini M, Dam M, Brandjes BD, Bachmeier CA, Anasetti C, Locke FL, Davila ML. 2020. Tumor Microenvironment Composition and Severe Cytokine Release Syndrome (CRS) Influence Toxicity in Patients with Large B-Cell Lymphoma Treated with Axicabtagene Ciloleucel. Clin Cancer Res 26:4823\u20134831.", "Li M, Chiang Y-L, Lyssiotis CA, Teater MR, Hong JY, Shen H, Wang L, Hu J, Jing H, Chen Z, Jain N, Duy C, Mistry SJ, Cerchietti L, Cross JR, Cantley LC, Green MR, Lin H, Melnick AM. 2019. Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis. Cancer Cell 35:916\u2013931.e9.", "Porpaczy E, Tripolt S, Hoelbl-Kovacic A, Gisslinger B, Bago-Horvath Z, Casanova-Hevia E, Clappier E, Decker T, Fajmann S, Fux DA, Greiner G, Gueltekin S, Heller G, Herkner H, Hoermann G, Kiladjian J-J, Kolbe T, Kornauth C, Krauth M-T, Kralovics R, Muellauer L, Mueller M, Prchal-Murphy M, Putz EM, Raffoux E, Schiefer A-I, Schmetterer K, Schneckenleithner C, Simonitsch-Klupp I, Skrabs C, Sperr WR, Staber PB, Strobl B, Valent P, Jaeger U, Gisslinger H, Sexl V. 2018. Aggressive B-cell lymphomas in patients with myelofibrosis receiving JAK1/2 inhibitor therapy. Blood 132:694\u2013706.", "Teater M, Dominguez PM, Redmond D, Chen Z, Ennishi D, Scott DW, Cimmino L, Ghione P, Chaudhuri J, Gascoyne RD, Aifantis I, Inghirami G, Elemento O, Melnick A, Shaknovich R. 2018. AICDA drives epigenetic heterogeneity and accelerates germinal center-derived lymphomagenesis. Nat Commun 9:222.", "Raju S, Kretzmer LZ, Koues OI, Payton JE, Oltz EM, Cashen A, Polic B, Schreiber RD, Shaw AS, Markiewicz MA. 2016. NKG2D-NKG2D Ligand Interaction Inhibits the Outgrowth of Naturally Arising Low-Grade B Cell Lymphoma In Vivo. J Immunol 196:4805\u20134813.", "Rouhigharabaei L, Finalet Ferreiro J, Tousseyn T, van der Krogt J-A, Put N, Haralambieva E, Graux C, Maes B, Vicente C, Vandenberghe P, Cools J, Wlodarska I. 2014. Non-IG aberrations of FOXP1 in B-cell malignancies lead to an aberrant expression of N-truncated isoforms of FOXP1. PLoS One 9:e85851.", "Verma A, Jiang Y, Du W, Fairchild L, Melnick A, Elemento O. 2015. Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma. Genome Med 7:110.", "Bouquet J, Soloski MJ, Swei A, Cheadle C, Federman S, Billaud J-N, Rebman AW, Kabre B, Halpert R, Boorgula M, Aucott JN, Chiu CY. 2016. Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease. MBio 7:e00100\u201316.", "Jeong I, Lim J-H, Oh DK, Kim WJ, Oh Y-M. 2018. Gene expression profile of human lung in a relatively early stage of COPD with emphysema. Int J Chron Obstruct Pulmon Dis 13:2643\u20132655.", "Li M, Zhao L-M, Li S-L, Li J, Gao B, Wang F-F, Wang S-P, Hu X-H, Cao J, Wang G-Y. 2018. Differentially expressed lncRNAs and mRNAs identified by NGS analysis in colorectal cancer patients. Cancer Med 7:4650\u20134664.", "Deng X, Li S, Kong F, Ruan H, Xu X, Zhang X, Wu Z, Zhang L, Xu Y, Yuan H, Peng H, Yang D, Guan M. 2020. Long noncoding RNA PiHL regulates p53 protein stability through GRWD1/RPL11/MDM2 axis in colorectal cancer. Theranostics 10:265\u2013280.", "Lazar SB, Pongor L, Li XL, Grammatikakis I, Muys BR, Dangelmaier EA, Redon CE, Jang S-M, Walker RL, Tang W, Ambs S, Harris CC, Meltzer PS, Aladjem MI, Lal A. 2020. Genome-Wide Analysis of the FOXA1 Transcriptional Network Identifies Novel Protein-Coding and Long Noncoding RNA Targets in Colorectal Cancer Cells. Mol Cell Biol 40.", "Lu S, Zhu N, Guo W, Wang X, Li K, Yan J, Jiang C, Han S, Xiang H, Wu X, Liu Y, Xiong H, Chen L, Gong Z, Luo F, Hou W. 2020. RNA-Seq Revealed a Circular RNA-microRNA-mRNA Regulatory Network in Hantaan Virus Infection. Front Cell Infect Microbiol 10:97.", "Li Y, Quan C, Xing W, Wang P, Gao J, Zhang Z, Jiang X, Ma C, Carr MJ, He Q, Gao L, Bi Y, Tang H, Shi W. 2020. Rapid humoral immune responses are required for recovery from haemorrhagic fever with renal syndrome patients. Emerg Microbes Infect 9:2303\u20132314.", "Blanco-Melo D, Nilsson-Payant BE, Liu W-C, Uhl S, Hoagland D, M\u00f8ller R, Jordan TX, Oishi K, Panis M, Sachs D, Wang TT, Schwartz RE, Lim JK, Albrecht RA, tenOever BR. 2020. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell 181:1036\u20131045.e9.", "Jenks SA, Cashman KS, Zumaquero E, Marigorta UM, Patel AV, Wang X, Tomar D, Woodruff MC, Simon Z, Bugrovsky R, Blalock EL, Scharer CD, Tipton CM, Wei C, Lim SS, Petri M, Niewold TB, Anolik JH, Gibson G, Lee FE-H, Boss JM, Lund FE, Sanz I. 2018. Distinct Effector B Cells Induced by Unregulated Toll-like Receptor 7 Contribute to Pathogenic Responses in Systemic Lupus Erythematosus. Immunity 49:725\u2013739.e6.", "Scharer CD, Blalock EL, Mi T, Barwick BG, Jenks SA, Deguchi T, Cashman KS, Neary BE, Patterson DG, Hicks SL, Khosroshahi A, Eun-Hyung Lee F, Wei C, Sanz I, Boss JM. 2019. Epigenetic programming underpins B cell dysfunction in human SLE. Nat Immunol 20:1071\u20131082.", "Wang S, Wang J, Kumar V, Karnell JL, Naiman B, Gross PS, Rahman S, Zerrouki K, Hanna R, Morehouse C, Holoweckyj N, Liu H, Autoimmunity Molecular Medicine Team, Manna Z, Goldbach-Mansky R, Hasni S, Siegel R, Sanjuan M, Streicher K, Cancro MP, Kolbeck R, Ettinger R. 2018. IL-21 drives expansion and plasma cell differentiation of autoreactive CD11cT-bet B cells in SLE. Nat Commun 9:1758.", "Zhang X, Chu H, Wen L, Shuai H, Yang D, Wang Y, Hou Y, Zhu Z, Yuan S, Yin F, Chan JF-W, Yuen K-Y. 2020. Competing endogenous RNA network profiling reveals novel host dependency factors required for MERS-CoV propagation. Emerg Microbes Infect 9:733\u2013746.", "Yuan S, Chu H, Chan JF-W, Ye Z-W, Wen L, Yan B, Lai P-M, Tee K-M, Huang J, Chen D, Li C, Zhao X, Yang D, Chiu MC, Yip C, Poon VK-M, Chan CC-S, Sze K-H, Zhou J, Chan IH-Y, Kok K-H, To KK-W, Kao RY-T, Lau JY-N, Jin D-Y, Perlman S, Yuen K-Y. 2019. SREBP-dependent lipidomic reprogramming as a broad-spectrum antiviral target. Nat Commun 10:120.", "Aprianto R, Slager J, Holsappel S, Veening J-W. 2016. Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection. Genome Biol 17:198.", "Kuipers K, Lokken KL, Zangari T, Boyer MA, Shin S, Weiser JN. 2018. Age-related differences in IL-1 signaling and capsule serotype affect persistence of Streptococcus pneumoniae colonization. PLoS Pathog 14:e1007396.", "Jochems SP, Marcon F, Carniel BF, Holloway M, Mitsi E, Smith E, Gritzfeld JF, Sol\u00f3rzano C, Rein\u00e9 J, Pojar S, Nikolaou E, German EL, Hyder-Wright A, Hill H, Hales C, de Steenhuijsen Piters WAA, Bogaert D, Adler H, Zaidi S, Connor V, Gordon SB, Rylance J, Nakaya HI, Ferreira DM. 2018. Inflammation induced by influenza virus impairs human innate immune control of pneumococcus. Nat Immunol 19:1299\u20131308.", "Weight CM, Venturini C, Pojar S, Jochems SP, Rein\u00e9 J, Nikolaou E, Sol\u00f3rzano C, Noursadeghi M, Brown JS, Ferreira DM, Heyderman RS. 2019. Microinvasion by Streptococcus pneumoniae induces epithelial innate immunity during colonisation at the human mucosal surface. Nat Commun 10:3060.", "Lamers MM, Beumer J, van der Vaart J, Knoops K, Puschhof J, Breugem TI, Ravelli RBG, Paul van Schayck J, Mykytyn AZ, Duimel HQ, van Donselaar E, Riesebosch S, Kuijpers HJH, Schipper D, van de Wetering WJ, de Graaf M, Koopmans M, Cuppen E, Peters PJ, Haagmans BL, Clevers H. 2020. SARS-CoV-2 productively infects human gut enterocytes. Science 369:50\u201354.", "Duan F, Guo L, Yang L, Han Y, Thakur A, Nilsson-Payant BE, Wang P, Zhang Z, Ma CY, Zhou X, Han T, Zhang T, Wang X, Xu D, Duan X, Xiang J, Tse H-F, Liao C, Luo W, Huang F-P, Chen Y-W, Evans T, Schwartz RE, tenOever B, Ho DD, Chen S, Lian Q, Chen HJ. 2020. Modeling COVID-19 with Human Pluripotent Stem Cell-Derived Cells Reveals Synergistic Effects of Anti-inflammatory Macrophages with ACE2 Inhibition Against SARS-CoV-2. Res Sq https://doi.org/10.21203/rs.3.rs-62758/v1.", "Vanderheiden A, Ralfs P, Chirkova T, Upadhyay AA, Zimmerman MG, Bedoya S, Aoued H, Tharp GM, Pellegrini KL, Manfredi C, Sorscher E, Mainou B, Lobby JL, Kohlmeier JE, Lowen AC, Shi P-Y, Menachery VD, Anderson LJ, Grakoui A, Bosinger SE, Suthar MS. 2020. Type I and Type III Interferons Restrict SARS-CoV-2 Infection of Human Airway Epithelial Cultures. J Virol 94."]}