Gammaproteobacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB12075 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Infection is a dialog between the pathogen and the host. Understanding the molecular basis of infection requires understanding the responses and adaptations of both the pathogen and host as a consequence of this dialog. We studied Mtb infection in human THP-1 cells by transcriptomics profiling of host expression over the course of an acute to anestablished infection. TbSysBio (National Institute of Allergy and Infectious Diseases, National Institute of Health)
2014-12-31 | GSE51029 | GEO
Project description:A total of 38 flash-frozen breast cancer tissues were collected from three medical centers in the Netherlands (i.e. National Cancer institute: n=19; Radboud University Medical Center: n=4; Erasmus University Medical Center: n=15). All tissues were analyzed as laser capture microdissected (LCM) and whole samples (whole tissue lysate: WTL). All gathered samples were primary estrogen receptor (ER) tumors, which were subdivided in two patient groups according to outcome to first line (i.e. recurrent disease setting) tamoxifen therapy based on time-to-progression (TTP): patients which manifested progression of disease before (i.e. TTP <=) 6 months were defined as "poor outcome", while patients which manifested progression after (i.e. TTP>) 6 months were defined as "good outcome". All patients did not receive adjuvant hormonal therapy (i.e. tamoxifen or aromatase inhibitors post-surgical resection of primary tumor). The LCM subset derives from PXD000484 (Erasmus Medical Center samples) and PXD000485 (National Cancer Institute and Radboud University Medical Center).
2016-03-31 | PXD002381 | Pride
Project description:Ten human ovarian cancer cell lines were kindly provided as follows: an ovarian serous adenocarcinoma cell line, SKOV3 (Dr. N. Nagai, Hiroshima University, Hiroshima, Japan); KF28 and its TXL/CDDP-resistant variant (Dr. Y. Kikuchi, National Defense Medical College, Saitama, Japan); KF, SHIN3 and 5 ovarian clear cell adenocarcinoma cell lines, KK, TAYA, RMG-1, OVISE and OVTOKO (Dr. M. Suzuki, Jichi Medical School, Tochigi, Japan). All cell lines were cultured in RPMI 1640 medium (Life Technologies, Inc., Grand Island, NY) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) in a humidified atmosphere of 5% CO2 and maintained in continuous exponential growth by passage every 3 days. Exponentially growing cultured cells were collected after two-washings with PBS. The cell pellets were immediately frozen in liquid nitrogen, and stored until use. Total RNA was extracted using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA). The quality of the RNA was checked using Agilent Technologies 2100 Bioanalyzer (Agilent, Palo Alto, CA). CodeLink Expression Bioarray System (Amersham Bioscience, Tokyo, Japan) was used according to the manufacturer’s protocol. Briefly, first-strand cDNA was generated from 1 microgram of total RNA of each cell line using reverse transcriptase and a T7 primer, and then second-strand cDNA was produced using DNA polymerase mix and RNase H. Complementary RNA (cRNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and biotin-11-UTP (Perkin Elmer, Boston, MA), which was quantified by spectrometry and checked using Agilent Technologies 2100 Bioanalyzer (Agilent). Ten-microgram of cRNA was then fragmented and hybridized to a Uniset Human 20K I Bioarray containing 19,881 probes with positive and negative bacterial control probes. After hybridization, the arrays were rinsed and labeled with Streptavidin-Cy5, scanned using Agilent DNA Microarray Scanner (Agilent), then analyzed with CodeLink Expression Analysis Software ver.2.3. Expression levels were normalized to the median expression value of the whole array spots. Keywords: parallel sample
2005-12-31 | GSE3001 | GEO
Project description:Genome sequencing of Gram-negative bacteria collected in Hiroshima
| PRJDB12041 | ENA
Project description:This series contains microarrays for ten types of mouse lymphomas, nude mouse purified resting B cells, and nude mouse purified B cells stimulated with LPS. Microarray chips containing 70-mer oligonucleotides representing approximately 6,800 genes were prepared by the Microarray Center of the National Institute of Allergy and Infectious Diseases, Bethesda, MD. Keywords = mouse Keywords = lymphoma Keywords = B cells Keywords: other
2004-12-01 | GSE1908 | GEO
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:The Genotype-Tissue Expression (GTEx) project is a collaborative effort that aims to identify correlations between genotype and tissue-specific gene expression levels that will help identify regions of the genome that influence whether and how much a gene is expressed. GTEx is funded through the Common Fund, and managed by the NIH Office of the Director in partnership with the National Human Genome Research Institute, National Institute of Mental Health, the National Cancer Institute, the National Center for Biotechnology Information at the National Library of Medicine, the National Heart, Lung and Blood Institute, the National Institute on Drug Abuse, and the National Institute of Neurological Diseases and Stroke, all part of NIH. This series of 837 samples represents multiple tissues collected from 102 GTEX donors and 1 control cell line. In total, 30 tissue sites are represented including Adipose, Artery, Heart, Lung, Whole Blood, Muscle, Skin, and 11 brain subregions. RNA-seq expression data, robust clinical data, pathological annotations, and genotypes are also available for these samples from dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v2.p1) and the GTEx portal (www.broadinstitute.org/gtex). While GTEx is no longer generating Affymetrix expression data, donor enrollment continues and is expected to reach 1,000 by the end of 2015. Updates to the GTEx data in dbGaP and the GTEx Portal will be made periodically. contributor: GTEx Laboratory, Data Analysis, and Coordinating Center (LDACC) contributor: The Broad Institute of MIT and Harvard (LDACC PIs: Kristin Ardlie and Gaddy Getz)
2013-04-09 | GSE45878 | GEO
Project description:This series contains microarrays for ten types of mouse lymphomas, nude mouse purified resting B cells, and nude mouse purified B cells stimulated with LPS. Microarray chips containing 70-mer oligonucleotides representing approximately 6,800 genes were prepared by the Microarray Center of the National Institute of Allergy and Infectious Diseases, Bethesda, MD. Keywords = mouse Keywords = lymphoma Keywords = B cells
2004-11-30 | E-GEOD-1908 | biostudies-arrayexpress
Project description:1Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. 2Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA. 3Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. 4CCTS Bioinformatic Program, The Rockefeller University, New York, NY 10065, USA. 5State Key Laboratory of Genetic Engineering & Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
2021-06-30 | GSE84157 | GEO
Project description:Japan Antimicrobial Resistant Bacterial Surveillance on Gram-negative Rods: JARBS-GNR
| PRJDB10842 | ENA