Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative genomic hybridization of 33 group I. Clostridium botulinum strains reveals 2 clusters with different resistance to cadmium and arsenic

ABSTRACT: genomic comparison of group I C.botulinum strains

ORGANISM(S): Clostridium botulinum

SUBMITTER: Miia Lindström

PROVIDER: E-TABM-309 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Comparative genomic hybridization analysis of two predominant Nordic group I (proteolytic) Clostridium botulinum type B clusters.

Lindström Miia M Hinderink Katja K Somervuo Panu P Kiviniemi Katri K Nevas Mari M Chen Ying Y Auvinen Petri P Carter Andrew T AT Mason David R DR Peck Michael W MW Korkeala Hannu H

Applied and environmental microbiology 20090306 9

Comparative genomic hybridization analysis of 32 Nordic group I Clostridium botulinum type B strains isolated from various sources revealed two homogeneous clusters, clusters BI and BII. The type B strains differed from reference strain ATCC 3502 by 413 coding sequence (CDS) probes, sharing 88% of all the ATCC 3502 genes represented on the microarray. The two Nordic type B clusters differed from each other by their response to 145 CDS probes related mainly to transport and binding, adaptive mech ...[more]

PMID: 19270141

Similar Datasets

Transcription profiling of human dormant and angiogenic breast cancer, osteosarcoma, liposarcoma and brain tumor cell lines

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. Referneces: 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. Prolonged dormancy of human liposarcoma is associated with impaired tumor angiogenesis. FASEB J. 2006 May;20(7):947-9. Naumov GN, Bender E, Zurakowski D, Kang SY, Sampson D, Flynn E, Watnick RS, Straume O, Akslen LA, Folkman J, Almog N. A model of human tumor dormancy: an angiogenic switch from the nonangiogenic phenotype. J Natl Cancer Inst. 2006 Mar 1;98(5):316-25.

2009-02-03 | E-TABM-390 | biostudies-arrayexpress

Transcription profiling time series of human HeLa cells cultivated while sterol depleted from the medium

Project description:The aim of the experiment was to identify novel genes with relevance to cellular cholesterol metabolism. HeLa cells were cultivated while sterol was depleted from the medium by applying 2-Hydroxypropyl-cyclodextrin. RNA for expression profiling was isolated 3h, 4.5h and 6h after depletion.

2008-12-17 | E-TABM-599 | biostudies-arrayexpress

Transcription profiling of human dermal microvascular endothelial, fibroblast, and glioblastoma cells treated with mycophenolic acid

Project description:The effect of Mycophenolic acid on primary isolated human dermal microvascular endothelial (HDMVEC) and fibroblast cells as well as human glioblastoma brain tumor cell line (U87).

2008-06-25 | E-TABM-315 | biostudies-arrayexpress

Transcription profiling of irradiated human dermal microvascular endothelial cells

Project description:Human dermal microvascular endothelial cells (HDMVECs) were irradiated with 2 Gy or non-irradiated. Two methods of RNA isolation were used to comparatively analyze the miRNA status after radiation treatment.

2010-01-13 | E-TABM-617 | biostudies-arrayexpress

Transcription profiling of human neuro-invasive pancreatic tumors engineered in-vitro compared to less invasive parental cells

Project description:Perineural invasion (PNI) is considered to be a specific path for the spread of pancreatic cancer cells and PNI is thought to be one of the important factors that determine local recurrence after resection. In addition PNI has been implicated in the pain syndrome that affects the majority of pancreatic ductal adenocarcinoma (PDAC) patients. Here we aimed to investigate the transcriptional differences between neuro-invasive tumors engineered in-vitro compared to less invasive parental cells. Two colour differential hybridisations were performed with human universal reference total RNA (Clontech, #636538).

2009-04-01 | E-TABM-400 | biostudies-arrayexpress

Transcription profiling of Ectocarpus strain Esil32 porophyte and gametophyte stages in normal and mutant strains to analyse expression of two sets of genes previously identified as being putatively sporophyte-specific or gametophyte-specific

Project description:The aim of this experiment was to analyse the expression of two sets of genes identified as being putatively sporophyte-specific or gametophyte-specific by a suppressive subtraction hybridisation using cDNA from immature sporophytes and immature gametophytes of the Ectocarpus strain Esil32. The expression of these genes was analysed in the sporophyte and gametophyte generations of the life cycle (again using immature algae that had not yet produces zoidangia) and in the sporophyte generation of a mutant strain, immediate upright, that exhibits gametophyte-like characteristics during the sporophyte generation.

2007-08-01 | E-MEXP-848 | biostudies-arrayexpress

Transcription profiling of SET-2 deletion and wild type yeast on sense and anti-sense arrays

Project description:The presence of Set2-mediated methylation of H3K36 (K36me) correlates with transcription frequency throughout the yeast genome. K36me targets the Rpd3S complex to deacetylate transcribed regions and suppress cryptic transcription initiation at certain genes. Here, using a genome-wide approach, we report that the Set2-Rpd3S pathway is generally required for controlling acetylation at coding regions. When using acetylation as a functional read-out for this pathway, we discovered that longer genes and, surprisingly, genes transcribed at lower frequency exhibit a stronger dependency. Moreover, a systematic screen using high resolution tiling microarrays allowed us to identify a group of genes that rely on Set2-Rpd3S to suppress spurious transcripts. Interestingly, most of these genes are within the group that depend the same pathway to maintain a hypo-acetylated state at coding regions. These data highlight the importance of using the functional readout of histone codes to define the roles of specific pathways.

2009-03-03 | E-TABM-265 | biostudies-arrayexpress

Transcription profiling of fission yeast wild type and yox1 mutant strains

Project description:Transcription profiling of fission yeast /yox1/ deletion and genome wide location analysis of Yox1p and Cdc10p transcription factors reveal a negative feedback interaction: /yox1 /is transcriptionally activated by MBF, and Yox1p in turn transcriptionally represses the MBF target genes (including /yox1 /itself).

2009-08-20 | E-TABM-646 | biostudies-arrayexpress

Transcription profiling of human carcinoma in situs cells from testis compared to fetal gonocytes, oogonia and cultured embryonic stem cells

Project description:Abstract: Testicular cancers in young adult men derive from an inborn precursor lesion, called carcinoma in situ (CIS) of the testis. CIS cells are believed to arise from primordial germ cells or gonocytes that fail to differentiate into the male germ cell lineage, and show a remarkable resemblance to embryonic stem cells (ESC). With this study we aimed at further elucidating the origin of CIS using microarray analysis of genome-wide gene expression. CIS cells only constitute a small fraction of the tissue and therefore, to reduce contaminating RNA from other cell types, we developed a fast (160 sec) staining procedure specific for CIS and fetal germ cells. Highly enriched cell populations were obtained by laser microdissectioning. The expression profiles of CIS cells were compared to microdissected fetal gonocytes, oogonia and cultured ESC with and without genomic amplifications. The cell type most similar to CIS was the gonocytes indicating malignant transformation at this stage. The enriched cell populations allowed us to find unique expression patterns for the developmentally very related cell types. Analyses of the similarities and differences among the cell types may help us understand when and how the malignant transformation to CIS occurs.

2009-06-15 | E-TABM-488 | biostudies-arrayexpress

Transcription profiling of mouse aorta (whole or regions) from mice of different embryonic ages

Project description:In order to identify novel regulators of haematopoietic stem cell emergence in the mouse embryonic AGM region, 3 different types of gene expression comparisons were performed. In the first one, whole dorsal aortas from embryonic day (E) 11 embryos and E9 embryos were dissected, tissues from each time point were pooled and their expression profile compared (whole aorta (WA) E9 vs E11). 3 different pools/biological replicas were obtained for each time point, a dye swap was included in each experiment, a technical replicate was performed for each pool (including the dye swap) and 2 self-self hybridisation controls were included. In the second comparison, GFP+ cells were isolated by fluorescence-activated cell sorting from pooled E9 and E11 aortas from transgenic embryos that express GFP under the regulatory elements of the Ly-6A gene. We obtained one pool for each time point and compared their transcription profile (GFP E9 vs E11). This comparison also contained a dye swap and a technical replicate (also of the dye swap). In the third comparison, the E11 aorta was cut into 3 roughly equal parts. Pools were obtained of the middle region ("m") and the two outer regions, rostral and caudal, together ("r+c") and their expression profile compared (11AO m vs r+c). There was one pool of each population, and the experiment included a dye swap and a technical replicate (also of the dye swap) and one self-self hybridisation control. Isolated RNA was amplified by T7-mediated in vitro transcription, with one round for the first and the third comparison and two rounds for the second comparison (sorted GFP+ cells). Probes were labelled during the reverse transcription step. Within array normalisation was achieved with Lowess Smooth and between arrays with Z scores. ANOVA analysis identified differentially expressed genes and K means clustering was used to segregate them into upregulated and downregulated genes.

2009-06-06 | E-TABM-659 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data