Ontology highlight
ABSTRACT:
PROVIDER: PRJEB26000 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To determine genes regulated by HNF4G, we retrovirally infected LNCaP cells in triplicates to express HNF4G and empty vector as control. cDNA for HNF4G in pDONR201 vector was obtained from Harvard medical school Plasmid database (ID:HsCD00022314) and was cloned into an murine stem cell virus (MSCV)-based retroviral vector with puromycin selection marker (Addgene) using Gateway technology.
2017-11-01 | GSE85244 | GEO
Project description:This project sought to identify the features in PEX5 required for interaction with the peroxisomal PEX2-PEX10-PEX12 ubiquitin ligase complex. Peroxisomes equilibrated with different PEX5 mutants (i.e., C11A, AH1, AH2) were purified from Xenopus egg extract, solubilized in digitonin, and PEX5-associated material was immunoprecipitated via a C-terminal FLAG tag. PEX5 without a FLAG tag was used as a negative control. PEX5-interacting peroxins were identified by LC-MS/MS at the Taplin Mass Spectrometry Facility at Harvard Medical School.
2022-08-16 | PXD035105 | Pride
Project description:Canonical protein phosphatase 3 (Ppp3) / calcineurin signaling is central to numerous physiological processes. Here we provide evidence that calcineurin plays a pivotal role in controlling systemic energy and body weight homeostasis. Knockdown of calcineurin in Drosophila melanogaster led to a decrease in body weight, and energy stores, and increased energy expenditure. D. melanogaster piggyBac transposon insertion mutants (Thibault et al., 2004) (PBac{WH}CanA1[f01787] (Calcineurin A1) and PBac{WH}CanA-14F[f02374] (CanA at 14-F)) and the isogenic wildtype w1118 strain (BL-6326) were ordered from Exelixis Drosophila Stock Collection at Harvard Medical School.
2015-08-04 | GSE71701 | GEO
Project description:Introduction: Early life is characterized by heightened susceptibility to infections and is recognized as a major determinant of the immune system development and the overall health for the entire human lifespan. However, our knowledge of the development of the neonatal immune system is incomplete, limiting the development of novel preventative and therapeutic strategies, especially in newborns. To gain insight into the early immune system development and plasma proteome ontogeny, the Expanded Program on Immunization Consortium (EPIC) led by Professor Ofer Levy MD at Boston Children’s Hospital, Harvard Medical School and Tobias R. Kollmann Telethon Kids Institute, Australia as part of the Human Immunological Project Consortium (HIPC), established two independent cohorts of plasma from healthy newborns born by vaginal delivery during the first week of life. Methods: Blood samples were collected from 30 newborns in The Gambia (Medical Research Council Unit, The Gambia) at the day of birth (day of life, DOL 0) and at one of the follow-up visits on DOL1, DOL3, or DOL7. A similar validation cohort was collected in Papua New Guinea (PNG) (Institute for Medical Research, Papua New Guinea, Australasian) from 19 newborns. The plasma proteome was characterized by LC-MS on a Q Exactive using the proven and published plasma proteomics platform developed in the Steen Laboratory, led by Dr Hanno Steen, Director of Proteomics at Boston Children’s Hospital, Harvard Medical School, employing only microliter of plasma prepared in a 96-well plate format. The data was analyzed with MaxQuant. Results: We characterized 385 blood-plasma proteins. Utilizing the paired study design, we identified consistent changes related to ontogeny and cellular growth pathways in the blood-plasma proteome. Conclusion: This dataset allows for studying the early ontogeny of the plasma proteome, and in extension the early immune system development, in two independent healthy cohorts. Characterization of the plasma proteome may provide novel insight into new approaches to prevent, detect, and treat infectious diseases. Acknowledgements: We would like to thank all the participating families and all past and current members of the EPIC-HIPC, and the Steen Laboratory, without whom this study would not be possible. A special recognition goes to the teams who established the unique cohorts in The Gambia, by Professor Beate Kampmann and Dr Olubukola T. Idoko at The Gambia at the London School of Hygiene and Tropical Medicine, The Gambia, and in PNG, by Anita H.J. van der Biggelaar and William S. Pomat at Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia Perth, Australia.
2020-11-24 | PXD019817 | Pride
Project description:XBP1 is the transcriptino factor that is activated by the ER stress. XBP1 is known to induce the ER dexpansion and increase the expression of the ER chaperone genes to prtect the cell from the ER stress. We generated a mouse strain that lacked XBP1 specifically in the mouse intestine by breeding the XBP1flox mice with Villin-cre mice. Here we examined genes that are differentially expressed between WT and XBP1 KO mouse intestine to identify genes that are downstream of XBP1. Experiment Overall Design: Total RNAs were pooled from three mice of indicated genotypes. Microarray experiments were performed by using Affymetrix GeneChip® Mouse Genome 430 2.0 Array in Biopolymers Facility at Harvard Medical School.
2008-10-21 | E-GEOD-12038 | biostudies-arrayexpress
Project description:The Goal of this study is to explore the transcriptional differences between angiogenic and non-angiogenic tumors generated in Dr. Folkman's Lab, Harvard Medical School.<br>Referneces:<br>Almog N, Henke V, Flores L, Hlatky L, Kung AL, Wright RD, Berger R, Hutchinson L, Naumov GN, Bender E, Akslen LA, Achilles EG, Folkman J.<br>Prolonged dormancy of human liposarcoma is associated with impaired tumor angiogenesis.<br>FASEB J. 2006 May;20(7):947-9.<br><br>Naumov GN, Bender E, Zurakowski D, Kang SY, Sampson D, Flynn E, Watnick RS, Straume O, Akslen LA, Folkman J, Almog N.<br>A model of human tumor dormancy: an angiogenic switch from the nonangiogenic phenotype.<br>J Natl Cancer Inst. 2006 Mar 1;98(5):316-25.<br>
2009-02-03 | E-TABM-390 | biostudies-arrayexpress
Project description:Canonical protein phosphatase 3 (Ppp3) / calcineurin signaling is central to numerous physiological processes. Here we provide evidence that calcineurin plays a pivotal role in controlling systemic energy and body weight homeostasis. Knockdown of calcineurin in Drosophila melanogaster led to a decrease in body weight, and energy stores, and increased energy expenditure. D. melanogaster piggyBac transposon insertion mutants (Thibault et al., 2004) (PBac{WH}CanA1[f01787] (Calcineurin A1) and PBac{WH}CanA-14F[f02374] (CanA at 14-F)) and the isogenic wildtype w1118 strain (BL-6326) were ordered from Exelixis Drosophila Stock Collection at Harvard Medical School. RNA was isolated from the thorax of 50 flies per sample. Whole genome tiling gene arrays were utilized to reveal distinctly deregulated gene patterns that appeared in both mutants (n=4, respectively) as compared to the WT controls (n=4).
2015-08-04 | E-GEOD-71701 | biostudies-arrayexpress
Project description:The microarrays experiments was performed with the purpose of identify transcriptional networks activated by copper. This experiment correspond the work tituled Enterococcus faecalis reconfigure the activation of its transcriptional regulatory networks under different copper exposure levels (work in preparation).Mauricio Latorrea,b, Jessica Galloway-Peñac,d,e, Jung Hyeo Rhoc,d, Marko Budinichf, Barbara E. Murrayc,d,e, Alejandro Maassb,f, Mauricio Gonzáleza,b,f*. a INTA, Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile. b Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile. c Division of Infectious Disease, Department of Medicine, University of Texas Medical School, Houston, Texas, United States of America. d Center for the Study of Emerging and Reemerging Pathogens, University of Texas Medical School, Houston, Texas, United States of America. e Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America f Mathomics, Center for Mathematical Modeling (UMI2807CNRS), Santiago, Chile. * Corresponding author. Address: El Líbano 5524, Santiago 11, Chile. Fax: +56 (2) 2214030.
2013-11-12 | GSE45131 | GEO
Project description:Purpose: identifying genes responding to manganese depletion in Drosophila through whole transcriptome RNA-seq analyses Methods: 10 females and 10 males of wild type of the Oregon R-C genotype, were mated and allowed to lay eggs for five days on two variants of chemical diet (no manganese added or 5 ppm manganese). Parents were removed and recently-eclosed females were transferred to fresh medium, respectively, for another five days. 10 midguts were dissected in PBS and homogenized in TRIzol (Invitrogen). RNA extraction and purification was performed using the Direct-zol RNAMicroPrepkit (Zymo Research) method. two biological replicates were used for each dietary treatment group. The RNA was eluted with sterile water and each RNA solution was divided into two aliquots, one of which was freshly used to obtain an RNA Integrity Number (RIN) evaluation at the Harvard Medical School Biopolymers Facility. For samples with RIN > 6.7 and no RNA degradation, the other aliquot stored at -80°C was submitted for sequencing. Results: we identified differentially expressed genes responding to to manganese depletion in Drosophila.
2019-08-31 | GSE136676 | GEO
Project description:Whole cell pellets of Vibrio cholerae strains as described in Sit et al, 2022 (https://www.biorxiv.org/content/10.1101/2022.02.04.479082v1)
Proteomics performed by the Thermo Center for Multiplexed Proteomics at Harvard Medical School using a standard fractionated total proteomics workflow. Each RAW file corresponds to one analyzed fraction out of twelve.
Mapping of samples to tags is listed in the Supplementary File attached to this submission. BS001: WT V. cholerae (four replicates) BS553: delta secDF1 V. cholerae (three replicates). BS558, BS280, and BS338 correspond to strains analyzed in the same run but not presented in the manuscript.
2022-08-26 | MSV000090217 | MassIVE