دورية أكاديمية
أعرض في EDS

Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds.

التفاصيل البيبلوغرافية
العنوان: Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds.
المؤلفون: Dele-Oni DO; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Christianson KE; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Egri SB; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Vaca Jacome AS; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., DeRuff KC; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Mullahoo J; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Sharma V; Department of Genome Sciences, University of Washington, Seattle, WA, 98195, United States., Davison D; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Ko T; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States., Bula M; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States., Blanchard J; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States., Young JZ; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States., Litichevskiy L; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Lu X; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Lam D; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Asiedu JK; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Toder C; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Officer A; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Peckner R; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., MacCoss MJ; Department of Genome Sciences, University of Washington, Seattle, WA, 98195, United States., Tsai LH; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States., Carr SA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States., Papanastasiou M; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States. malpap@broadinstitute.org., Jaffe JD; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States. jjaffe@inzentx.com.; Inzen Therapeutics, Cambridge, MA, 02139, United States. jjaffe@inzentx.com.
المصدر: Scientific data [Sci Data] 2021 Aug 25; Vol. 8 (1), pp. 226. Date of Electronic Publication: 2021 Aug 25.
نوع المنشور: Dataset; Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101640192 Publication Model: Electronic Cited Medium: Internet ISSN: 2052-4463 (Electronic) Linking ISSN: 20524463 NLM ISO Abbreviation: Sci Data Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : Nature Publishing Group, 2014-
مواضيع طبية MeSH: Proteomics*, Antineoplastic Agents/*toxicity , Astrocytes/*drug effects , Astrocytes/*metabolism , Cardiotoxins/*toxicity , Protein Kinase Inhibitors/*toxicity, Cell Line, Tumor ; Humans ; Phosphorylation/drug effects ; Protein Processing, Post-Translational/drug effects ; Proteome
مستخلص: While gene expression profiling has traditionally been the method of choice for large-scale perturbational profiling studies, proteomics has emerged as an effective tool in this context for directly monitoring cellular responses to perturbations. We previously reported a pilot library containing 3400 profiles of multiple perturbations across diverse cellular backgrounds in the reduced-representation phosphoproteome (P100) and chromatin space (Global Chromatin Profiling, GCP). Here, we expand our original dataset to include profiles from a new set of cardiotoxic compounds and from astrocytes, an additional neural cell model, totaling 5300 proteomic signatures. We describe filtering criteria and quality control metrics used to assess and validate the technical quality and reproducibility of our data. To demonstrate the power of the library, we present two case studies where data is queried using the concept of "connectivity" to obtain biological insight. All data presented in this study have been deposited to the ProteomeXchange Consortium with identifiers PXD017458 (P100) and PXD017459 (GCP) and can be queried at https://clue.io/proteomics .
(© 2021. The Author(s).)
References: Nature. 2019 May;569(7757):503-508. (PMID: 31068700)
PLoS One. 2015 Jun 15;10(6):e0129242. (PMID: 26075891)
Nat Methods. 2020 Dec;17(12):1237-1244. (PMID: 33199889)
Biochem Biophys Res Commun. 1986 Mar 13;135(2):397-402. (PMID: 3457562)
Sci Data. 2021 Aug 25;8(1):226. (PMID: 34433823)
NAR Genom Bioinform. 2019 Oct 30;2(1):lqz010. (PMID: 33575562)
Nat Commun. 2014 Jul 18;5:4430. (PMID: 25034944)
J Neurosci. 2011 Feb 16;31(7):2615-23. (PMID: 21325529)
Nature. 2000 Feb 3;403(6769):503-11. (PMID: 10676951)
Expert Rev Anticancer Ther. 2018 Dec;18(12):1249-1270. (PMID: 30259761)
Neuron. 2018 Jun 27;98(6):1141-1154.e7. (PMID: 29861287)
N Engl J Med. 2013 Jul 25;369(4):341-50. (PMID: 23883379)
Trends Pharmacol Sci. 2013 Sep;34(9):508-17. (PMID: 23928289)
Curr Protein Pept Sci. 2015;16(6):559-70. (PMID: 25854924)
Cancer Cell. 2017 Feb 13;31(2):225-239. (PMID: 28196595)
Front Cell Neurosci. 2014 Dec 11;8:427. (PMID: 25565961)
Lancet Neurol. 2009 Nov;8(11):1056-72. (PMID: 19833297)
Nature. 2000 Aug 17;406(6797):747-52. (PMID: 10963602)
Cell Syst. 2018 Apr 25;6(4):424-443.e7. (PMID: 29655704)
Nature. 2000 Aug 3;406(6795):532-5. (PMID: 10952316)
Cell Death Differ. 2010 Aug;17(8):1238-43. (PMID: 20467440)
Cell. 2017 Nov 30;171(6):1437-1452.e17. (PMID: 29195078)
Biochem Biophys Res Commun. 2014 Dec 5;455(1-2):24-34. (PMID: 25111821)
Int J Mol Med. 2017 Aug;40(2):271-280. (PMID: 28656226)
J Proteome Res. 2014 Sep 5;13(9):4205-10. (PMID: 25102069)
Glia. 2009 Sep;57(12):1251-64. (PMID: 19373940)
J Neuroinflammation. 2018 Nov 30;15(1):331. (PMID: 30501627)
Nature. 2000 Aug 3;406(6795):536-40. (PMID: 10952317)
N Engl J Med. 2012 Aug 16;367(7):647-57. (PMID: 22894577)
Eur J Neurosci. 2016 Nov;44(10):2858-2870. (PMID: 27564458)
Front Aging Neurosci. 2015 Jan 06;6:342. (PMID: 25610395)
Immunity. 2017 Jun 20;46(6):957-967. (PMID: 28636962)
Cell Syst. 2018 Jan 24;6(1):13-24. (PMID: 29199020)
Epigenomics. 2016 Jan;8(1):77-84. (PMID: 26698557)
Nat Genet. 2013 Nov;45(11):1386-91. (PMID: 24076604)
NPJ Precis Oncol. 2017 Sep 12;1(1):31. (PMID: 29872712)
Open Biol. 2017 Dec;7(12):. (PMID: 29237809)
J Am Soc Mass Spectrom. 2019 Apr;30(4):669-684. (PMID: 30671891)
Eur J Neurosci. 2009 Jul;30(1):1-8. (PMID: 19508697)
Methods. 2015 Jan 15;72:57-64. (PMID: 25448295)
Nat Immunol. 2016 Sep;17(9):1016-24. (PMID: 27478938)
Mol Cell Proteomics. 2018 Jun;17(6):1239-1244. (PMID: 29487113)
N Engl J Med. 1999 Nov 18;341(21):1565-71. (PMID: 10564685)
Front Neuroanat. 2018 Dec 06;12:104. (PMID: 30574073)
Nat Rev Neurol. 2016 Jul;12(7):379-92. (PMID: 27340022)
Curr Genomics. 2013 Apr;14(2):91-110. (PMID: 24082820)
Bioinformatics. 2010 Apr 1;26(7):966-8. (PMID: 20147306)
J Proteome Res. 2006 Feb;5(2):240-7. (PMID: 16457588)
Nat Biotechnol. 2010 Oct;28(10):1069-78. (PMID: 20944599)
Sci Signal. 2018 May 15;11(530):. (PMID: 29764989)
Science. 1999 Oct 15;286(5439):531-7. (PMID: 10521349)
Molecules. 2015 Mar 02;20(3):3898-941. (PMID: 25738536)
Nat Neurosci. 2018 Apr;21(4):497-505. (PMID: 29507413)
Nucleic Acids Res. 2020 Jan 8;48(D1):D1145-D1152. (PMID: 31686107)
Prog Neurobiol. 2019 Mar;174:36-52. (PMID: 30599178)
J Mol Biol. 2014 Oct 9;426(20):3389-412. (PMID: 24709417)
Science. 2006 Sep 29;313(5795):1929-35. (PMID: 17008526)
Mol Cell Proteomics. 2016 May;15(5):1622-41. (PMID: 26912667)
Nat Protoc. 2012 Oct;7(10):1836-46. (PMID: 22976355)
Methods Mol Med. 2004;88:43-55. (PMID: 14634217)
معلومات مُعتمدة: U24 CA210986 United States CA NCI NIH HHS; U54-HG008097 U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI); U54 HG008097 United States HG NHGRI NIH HHS; U01 CA214125 United States CA NCI NIH HHS; U01-CA214125 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI); U24-CA210986 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
المشرفين على المادة: 0 (Antineoplastic Agents)
0 (Cardiotoxins)
0 (Protein Kinase Inhibitors)
0 (Proteome)
تواريخ الأحداث: Date Created: 20210826 Date Completed: 20210930 Latest Revision: 20231107
رمز التحديث: 20231107
مُعرف محوري في PubMed: PMC8387426
DOI: 10.1038/s41597-021-01008-4
PMID: 34433823
قاعدة البيانات: MEDLINE
الوصف
تدمد:2052-4463
DOI:10.1038/s41597-021-01008-4