Engineered Microalgal Biofilms
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA589649 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR10492857_1.fastq.gz | Fastqsanger.gz | |||
| SRR10492857_2.fastq.gz | Fastqsanger.gz | |||
| SRR10492858_1.fastq.gz | Fastqsanger.gz | |||
| SRR10492858_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 75 |
Similar Datasets
Project description:Diabetic wound biofilms raw sequence reads
| PRJNA304940 | ENA
Project description:Drinking water biofilms (lead) Raw sequence reads
| PRJNA663268 | ENA
Project description:drinking water and biofilms Raw sequence reads
| PRJNA643656 | ENA
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:Microarrays offer a comprehensive tool for a system-wide analysis of cell functioning based on the simultaneous detection of the activity of thousands of genes. While transcriptome analyses are usually related with the study of gene expression and regulation within single species in laboratory experiments or environmental samples, in the present study, the possibility of studying gene expression in river biofilm communities was explored. To this aim a Functional Gene array (FGA), based on consensus sequences from genes of key physiological processes, was designed including 83 functional genes chosen to reflect several essential biochemical pathways and specific stress response pathways. Probes of these genes were designed from consensus sequences from up to 6 microalgal species (diatoms and chlorophytes). Furthermore, species specific probes were included resulting in 1556 unique oligonucleotide probes for 83 different genes. RNA extracted from Chlamydomonas reinhardtii, Scenedesmus vacuolatus and multi-species biofilms was then hybridized to oligonucleotide arrays at different hybridization temperatures (55, 60 and 65ºC). Signal intensity was affected by sequence divergence but results showed that hybridisation temperature of 55ºC allowed a good compromise between cross-hybridization and specificity. Due to the limited number of probes and available sequence information the designed FGAs is at present particularly useful for the comparison of similar biofilms exposed to different conditions in laboratory experimental studies.
2012-12-31 | GSE22496 | GEO
Project description:Microarrays offer a comprehensive tool for a system-wide analysis of cell functioning based on the simultaneous detection of the activity of thousands of genes. While transcriptome analyses are usually related with the study of gene expression and regulation within single species in laboratory experiments or environmental samples, in the present study, the possibility of studying gene expression in river biofilm communities was explored. To this aim a Functional Gene array (FGA), based on consensus sequences from genes of key physiological processes, was designed including 83 functional genes chosen to reflect several essential biochemical pathways and specific stress response pathways. Probes of these genes were designed from consensus sequences from up to 6 microalgal species (diatoms and chlorophytes). Furthermore, species specific probes were included resulting in 1556 unique oligonucleotide probes for 83 different genes. RNA extracted from Chlamydomonas reinhardtii, Scenedesmus vacuolatus and multi-species biofilms was then hybridized to oligonucleotide arrays at different hybridization temperatures (55, 60 and 65ºC). Signal intensity was affected by sequence divergence but results showed that hybridisation temperature of 55ºC allowed a good compromise between cross-hybridization and specificity. Due to the limited number of probes and available sequence information the designed FGAs is at present particularly useful for the comparison of similar biofilms exposed to different conditions in laboratory experimental studies. Nine samples were used, three were extracted from biofilm communities and hybridized at 55, 60 and 65 ºC, respectively; three were extracted from Scenedesmus vacuolatus and hybridized at 55, 60 and 65 ºC, respectively; and the three last ones were extracted from Chlamydomonas reinhardtii and hybridized at 55, 60 and 65 ºC
2012-12-31 | E-GEOD-22496 | biostudies-arrayexpress
Project description:To explain enhanced biofilm formation and increased dissemination of S. epidermidis in mixed-species biofilms, microarrays were used to explore differential gene expression of S. epidermidis in mixed-species biofilms. One sample from single species biofilm (S1) and mixed-species biofilm (SC2) were excluded from analyses for outliers. We observed upregulation (2.7%) and down regulation (6%) of S. epidermidis genes in mixed-species biofilms. Autolysis repressors lrgA and lrgB were down regulated 36-fold and 27-fold respectively and was associated with increased eDNA possibly due to enhanced autolysis in mixed-species biofilms. These data suggest that bacterial autolysis and release of eDNA in the biofilm matrix may be responsible for enhancement and dissemination of mixed-species biofilms of S. epidermidis and C. albicans. Staphylococcal gene expression in mixed-species biofilms with Candida and in single species biofilms of S. epidermidis were analyzed. The experiment was repeated thrice on 3 different days (3 biological replicates each for single species biofilms of S. epidermidis and mixed-species biofilms). Only 2 biological replicates were analyzed and one biological replicate was not analyzed (S1 and SC1 - raw data files are provided on the Series record). Single species biofilms of S. epidermidis (strain 1457) and C. albicans (strain 32354) and mixed-species biofilms were formed on 6-well tissue culture plates. Five ml of organism suspensions (O.D. 0.3, S. epidermidis 107 CFU/ml or C. albicans 105 CFU/ml) or 2.5 ml each for mixed-species biofilms for 24 hr. RNA was harvested from single species and mixed-species biofilms.
2012-02-28 | E-GEOD-35438 | biostudies-arrayexpress
Project description:biofilms on various plastics in the Niagara River Raw sequence reads
| PRJNA490293 | ENA