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PROVIDER: PRJNA1055132 | ENA |
REPOSITORIES: ENA
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Project description:Sixteen paired matched samples from primary breast cancers and brain metastases diagnosed between April 1, 2001 and December 31, 2012 were collected from 8 institutions. Brain metastases were identified based on magnetic resonance imaging and/or computed tomography findings. The clinical characteristics of all the patients were obtained from their medical records. This study was approved by the institutional review board of each participating institute (Tokai University School of Medicine; National Hospital Organization Osaka National Hospital; Kinki University School of Medicine; Niigata Cancer Center Hospital; Shizuoka General Hospital; Hokkaido Cancer Center; National Hospital Organization, Tokyo Medical Center; and Gunma Prefectural Cancer Center). Matching primary breast cancers and brain metastases Formalin-Fixed Paraffin-Embedded (FFPE) specimens for gene expression analysis were collected into RNA. RNA from specimens was isolated, and quantity and quality of the each RNA was using an Agilent 2100 Bioanalyzer (Agilent Technologies). Genome-wide expression levels of transcripts were analyzed using the Affymetrix U133A gene chips (Affymetrix) according to the manufacture’s instructions.
2019-09-25 | GSE125989 | GEO
Project description:Trans-kingdom mimicry underlies ribosome customization by a poxvirus kinase
Sujata Jha*1, Madeline G. Rollins*1, Gabriele Fuchs2, Dean J. Procter1, Elizabeth A. Hall3, Kira Cozzolino3, Peter Sarnow4, Jeffrey N. Savas3 and Derek Walsh1
1Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. 2The RNA Institute, Department of Biological Sciences, University of Albany-SUNY, Albany, NY 12222, USA. 3Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. 4Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
2017-03-21 | MSV000080661 | MassIVE
Project description:Authors: Marc P. Forrest1,2, Marc Dos Santos1,2, Nicolas H. Piguel1,2, Yi-Zhi Wang3, Nicole A. Hawkins4, Vikram A. Bagchi1,2, Leonardo E. Dionisio1,2, Sehyoun Yoon1,2, Dina Simkin3,4, Maria Dolores Martin-de-Saavedra1,2, Ruoqi Gao1,2, Katherine E. Horan1,2, Alfred L. George Jr.2,4, Mark S. LeDoux5,6, Jennifer A. Kearney 2,4, Jeffrey N. Savas2,3, Peter Penzes1,2*
Affiliations:
1Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
2Center for Autism and Neurodevelopment, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
3Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
4Department of Pharmacology Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
5Department of Psychology, University of Memphis, Memphis, TN 38152, USA.
6Veracity Neuroscience LLC, Memphis, TN 38157, USA.
*Correspondence to: p.penzes@northwestern.edu
2022-12-12 | MSV000090884 | MassIVE
Project description:To identify gene regulatory regions in the cochlea, we FACS-sorted biological duplicates of epithelial cells (CD326+; including hair cells and supporting cells) and non-epithelial cells (CD326-; predominantly mesenchymal cells) from mouse cochlea at postnatal day 2 and performed ATAC-seq to identify open chromatin regions in each cell type. CD-1 timed-pregnant females were purchased from Charles River (Maryland). At postnatal day 2, the mice were euthanized and their temporal bone removed. Cochlear ducts from 20 mice were harvested, pooled and processed for Fluorescence-activated cell sorting (FACS). Briefly, single-cell suspensions were obtained and incubated with an APC-conjugated anti-CD326 (1:2000, BioLegend) to label epithelial cells. Cells were sorted into cochlear CD326 (+) cells (epithelial) and cochlear CD326 (-) cells (non-epithelial) by FACS using a BD FACS Aria II Cell Sorter (BD Biosciences) at the Flow Cytometry Facility, Center for Innovative Biomedical Resources (University of Maryland School of Medicine). 50,000 cells or 100,000 cells from each sample were further processed for ATAC-seq as described (Buenrostro et al. 2015. Curr. Prot. Mol. Med.) with the following modification: following the transposition reaction and purification step, a right side size selection (ratio 0.6) using SPRIselect (Beckman-Coulter, Indiana) was added before proceeding to the PCR amplification. This extra step resulted in the selection of DNA fragments between 150 bp to 700 bp.
2019-08-02 | GSE126129 | GEO
Project description:To find out the binding partners of EhRacJ, crosslinking and coimmunoprecipitation were performed. Then, eluted samples were submitted to Mass Spectrometry and Proteomics Core Facility, Johns Hopkins University School of Medicine and analyzed by mass spctrometry (shotgun proteomics). The coimmunoprecipitation and following analysis were conducted only a single time. You can find data of HA-EhRacJ from "2023_3_13_28_AM_FileSize_1261863517_Byte_F012933.mzid.gz", "2023_3_13_28_AM_FileSize_1261863517_Byte_F012933.mzid_2023_3_13_28_AM_File_Size__1261863517__Byte__F012933.MGF", "JS-E480-CS_230524_NozakiT_MS_DDA_S1_10pct.msf", "JS-E480-CS_230524_NozakiT_MS_DDA_S1_10pct.mzML", and "JS-E480-CS_230524_NozakiT_MS_DDA_S1_10pct.RAW". You can find data of pEhEx-HA (mock) from "2023_6_54_27_PM_FileSize_1168419053_Byte_F012936.mzid.gz", "2023_6_54_27_PM_File Size_1168419053_Byte_F012936.mzid_2023_6_54_27_PM_File_Size__1168419053__Byte__F012936.MGF", "JS-E480-CS_230524_NozakiT_MS_DDA_S4_10pct.msf", "JS-E480-CS_230524_NozakiT_MS_DDA_S4_10pct.mzML", and "JS-E480-CS_230524_NozakiT_MS_DDA_S4_10pct.RAW".
2024-06-20 | PXD051913 | Pride
Project description:Human lung samples from control and Down Syndrome prenatal patients were examined for Angiogenic Factors qPCR gene expression profiling was performed to analyze the gene expression differences between human prenatal Down Syndrome patients and age matched control samples. Human lung tissue was obtained from the University of Maryland, Baltimore through its NICHD Brain and Tissue Bank for Developmental Disorders (NICH Contract #HHSN275200900011C, Ref. No. N01-HD-9-0011). The studies included in this report were examined by an institutional review board (IRB) of the University of Colorado School of Medicine and the Childrenâs Hospital Colorado and are supported through the Decedent Research Certification Program All tissues were collected, stored and distributed while maintaining strict confidentiality, meeting appropriate HIPPA standards, with oversight provided by the University of Colorado IRB. Accordingly, limited clinical data is available. Small numbers of tissue were available for study, including 5 DS and 4 control flash frozen samples for quantitative RT-PCR. Total RNA was extracted from human lung tissue using the RNAqueous Total RNA Isolation Kit (Life Technologies AM1912). Samples were DNase I treated with the Ambion TURBO DNA-free kit (Invitrogen AM1907) and tested for quality with an Agilent 2100 Bioanalyzer. Samples were reverse-transcribed with RT2 First Strand Kit (Qiagen 330401). These samples were amplified using the RT2 Profiler PCR Array Human Angiogenesis (Qiagen PAHS-024Z). Quantitative RT-PCR was performed on a LightCycler LC480 System (Roche).
2016-08-01 | E-GEOD-81457 | biostudies-arrayexpress
Project description:Qionger He1, Erica D Arroyo2, Samuel N Smukowski3, Jian Xu, Claire Piochon1, Jeffrey N Savas3, Carlos Portera-Cailliau2 and Anis Contractor1,4*
1Department of Physiology & 3Department of Neurology, Northwestern University Feinberg School of Medicine; 2Departments of Neurology and Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 & 4Department of Neurobiology, Weinberg College of Arts and Sciences, Northwestern University, Chicago, IL 60611
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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:Gene expression was analyzed in brains of 4 male selectively-bred alcohol-preferring (P) rats (generation 63) and 3 male alcohol non-preferring (NP) rats (generation 62) that were obtained from Dr. Richard L. Bell, Indiana University School of Medicine, Indianapolis, IN. These rats had never been exposed to alcohol.
2011-04-19 | GSE15764 | GEO