Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

52 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array of Sulfolobus acidocaldarius and Sulfolobus solfataricus to study replication-biased genome organisation.

ABSTRACT: Determination of transcript abundance as a function of gene position on the cromosome

ORGANISM(S): Sulfolobus solfataricus

SUBMITTER: Magnus Lundgren

PROVIDER: E-MEXP-2770 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Sebastes melanops array 5K v1

Project description:We used a reference design with a dye swap. We used 6 experimental probes grouped by treatment and sample day. "Treatment" fish consisted of rockfish exposed to forced decompression resulting in barotrauma, followed by subsequent recompression to their original depth. Control fish did not experience forced decompression. Fish were sampled at day 3, day 15 and day 31 post-decompression.

2012-01-02 | E-MEXP-3087 | biostudies-arrayexpress

Disrupted circadian rhythms in a mouse model of schizophrenia

Project description:Disrupted circadian rhythms in a mouse model of schizophrenia

2012-03-01 | E-MEXP-3493 | biostudies-arrayexpress

EMT

Project description:three pairs of isogenic human mammary epithelial and fibroblast cells, were used to characterized cell type specific dna methylation using using methyla cytosin immunoprecipitation

2013-01-17 | E-MEXP-3651 | biostudies-arrayexpress

Transcription profiling of young and old yeast cells grown in pH controlled and uncontrolled media.

Project description:A 2 x 2 factorial design was used to elucidate the genome-wide transcriptional responses of old and young cells to the medium pH control. ?HO strain (BY4742 background) was cultivated batch-wise in SDC media and in fully controlled fermenters. pH was maintained at 4.5 via automatic NaOH addition for pH controlled case while this control was turned off for the unbuffered experiments. Samples of the young and old cells, collected at the 3rd and 7th day of the experiment respectively, were transferred to stimulating media containing fresh SDC medium prior to sample collection for transcriptional profiling.

2014-01-12 | E-MEXP-3972 | biostudies-arrayexpress

Transcriptional profiling by array of INSULIN-expressing cells derived from INS-GFP human embryonic stem cells under different differentiation and culture conditions

Project description:Differentiation of INSGFP/w hESCs using published protocols demonstrated that all GFP+ cells co-expressed insulin, confirming the fidelity of the reporter gene. INS-GFP+ cells also co-expressed glucagon and somatostatin, confirming prior studies regarding the polyhormonal nature of early hESC derived insulin-expressing cells. INSGFP/w hESCs were employed to develop a 96 well format spin Embryoid Body (EB) differentiation protocol that utilized the recombinant protein based fully defined medium, APEL. Like INS-GFP+ cells generated with other methods, those derived using the spin EB protocol expressed a collection of pancreatic related transcription factors including ISL1, PAX6 and NKX2.2. However, in contrast to previous methods, the spin EB protocol yielded INS-GFP+ cells that also co-expressed the beta-cell transcription factor, NKX6.1 and comprised a substantial proportion of monohormonal insulin+ cells.

2012-02-02 | E-MEXP-3378 | biostudies-arrayexpress

Chromatin immunoprecipitation of Arabidopsis to perform a chromosome-wide comparison of H3K9me2 distribution between nrpd1a-4_nrpd1b-11 and wild type plants

Project description:Chromatin immunoprecipitation and hybridization to a chromosome-wide DNA tiling array (ChIP-chip)was performed to compare the distribution pattern of H3K9me2 between nrpd1a-4_nrpd1b-11 and wild type. Experiments were done using two independent biological replicates.

2009-07-24 | E-MEXP-1727 | biostudies-arrayexpress

Rhythmic diel pattern of gene expression in maize

Project description:Here we studied the leaf transcriptome in maize, throughout a cycle of 10 h darkness and 14 h light to look for rhythmic patterns of gene expression.

2011-08-19 | E-MEXP-3212 | biostudies-arrayexpress

Transcription profiling of yeast strains lacking Met4 or Met4 cofactors at time points after sulfur limitation

Project description:All yeast strains used in this study (Table 1) are in the W303 background (ade2-1 can1-100, his3-1,15 leu2-3,112 trp1-1 ura3). For sulfur limitation microarray studies, WT, met4 delete, met31 delete met32 delete, cbf1 delete, and met28 delete strains were grown in minimal B-media [see Cherest, H., and Surdin-Kerjan, Y. (1992). Genetic analysis of a new mutation conferring cysteine auxotrophy in Saccharomyces cerevisiae: updating of the sulfur metabolism pathway. Genetics 130, p51-58 for B-media composition] supplemented with 0.5mM methionine as the sole sulfur source. An aliquot of cells was harvested for a t=0 time point while the remainder were filtered through a .22um Stericup filter (Millipore), then washed and resuspended in pre-warmed (30 C) B-media lacking any source of sulfur. Cells were harvested after 20, 40, and 80 minutes.

2009-11-30 | E-MEXP-2429 | biostudies-arrayexpress

Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe

Project description:In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery, such as Rdp1, is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the “unspliced” signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, andwe argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that expression of mid-meiotic genes is kept tightly off in vegetative cells by two independent ways: antisense transcription and Fkh2 repression.

2011-11-01 | E-MEXP-3414 | biostudies-arrayexpress

Transcript profiling of the wild type Arabidopsis grown under different photoperiods

Project description:Arabidopsis rosette leaves were harvested from plants grown under different photoperiods under 100 M-5mol photons m-2 s-1 at 20 M-0C. In the first experiment plants grown under short day conditions 8L/16D (8 h light / 16 h dark) for 4 weeks were compared with plants grown under long day (16L/8D) for 3 weeks. In the second experiment plants grown under 12L/12D for 2 weeks were compared with plants grown first 2 weeks under 12L/12D and then two days under short day (8L/16D) conditions.

2012-07-27 | E-MEXP-3331 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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