Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Cotton ovule development

ABSTRACT: Cotton ovule development, mutant vs wild type, Comparisons of DP16 0 dpa ovule Keywords: WildType vs Mutant 7 comparisons and one 0 dpa control. The 1A/DP16 & 4A/DP16 comparisons have 8 slides each, 4 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. The SL1-7-1/DP16 comparison has 6 slides, 3 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. The 5B/DP16, fl/Xu-142, OI/II+N & 53/DP16 comparisons have 4 slides each, 2 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. The 0 dpa control experiment has 3 slides , 3 Biological replicates, no technical replicates and no dye swapping.

ORGANISM(S): Gossypium hirsutum

SUBMITTER: Andrew Spriggs

PROVIDER: E-GEOD-3546 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Expression profiling identifies genes expressed early during lint fibre initiation in cotton.

Wu Yingru Y Machado Adriane C AC White Rosemary G RG Llewellyn Danny J DJ Dennis Elizabeth S ES

Plant & cell physiology 20051107 1

Cotton fibres are a subset of single epidermal cells that elongate from the seed coat to produce the long cellulose strands or lint used for spinning into yarn. To identify genes that might regulate lint fibre initiation, expression profiles of 0 days post-anthesis (dpa) whole ovules from six reduced fibre or fibreless mutants were compared with wild-type linted cotton using cDNA microarrays. Numerous clones were differentially expressed, but when only those genes that are normally expressed in ...[more]

PMID: 16278222

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Project description:A microarray analysis of wheat grain hardness For both the Heron and Falcon NIL, whole wheat heads were harvested at 6, 15 and 25 days post anthesis (DPA) from glass house grown material and stored at -80 OC. For the other wheat cultivars analysed, heads at approximately 9-10 DPA were used. Eight to ten developing caryopses at the same age and morphological stage of development were selected from a head to represent a sample. Seed collected from a different head represented a replicate sample. Total RNA was isolated from the whole seed following the method of Higgins et al. (1976) with the following modification to remove starch. After the lithium chloride precipitation, the RNA pellet was resuspended in 250 ?l water. Then 3.5 ?l of 3 M sodium acetate (pH 5.3) and 125 ?l ethanol were added and the sample was centrifuged for 10 minutes at 4 OC. The supernatant was transferred to a fresh tube and the RNA was ethanol-precipitated by the addition of 21.5 ?l of 3 M sodium acetate (pH 5.3) and 375 ?l ethanol. The recovery of RNA varied from 0.06-0.5 ?g RNA per mg of tissue and this was dependent on the developmental stage of the seeds used for extraction of the RNA. For the labelling procedure, 50 ?g of total RNA was used for both the Cy3 and Cy5 dyes (Amersham Pharmacia, UK), following the two-step labelling method of Schenk et al. (2000). The Cy3 control (hard wheat) and Cy5 sample (soft wheat) were swapped among the replicate experiments to minimise any bias in cDNA incorporation and photo-bleaching of the fluorescent dyes. The pre-hybridisation of the microarray slides, hybridisation of the target cDNA and subsequent washing of the slides to remove unbound target was performed as per the supplied protocol for the CMT-GAPSTM coated microscope slides (Corning USA). The slides were scanned with a GenePix 4000A microarray scanner (Axon Instruments, Union, CA, USA). The features were analysed using the GenePix Pro 4 software and unsatisfactorily segmented features were either manually adjusted or discarded to ensure the integrity of the data obtained.

Project description:Due to difficulties inherent in designating conservation units for effective species management and conservation, the use of multiple complementary sources of information is required to identify and assess the designation of conservation units based on the degree of variation among populations within a species. In this study, we combined estimates of microsatellite and transcriptomic variation to assess the population structure and potential for adaptive variation of threatened Atlantic salmon, Salmo salar, among rivers in the Bay of Fundy. In general, population structure identified by genetic differentiation was consistent with the patterns of variation in gene expression. Both data sets provided clear indication of strong regional differentiation between rivers located within the inner Bay of Fundy relative to rivers located within the outer Bay of Fundy or the Southern Uplands region. There was also support for more refined population structure; there was some differentiation in both microsatellite and gene expression patterns between salmon from rivers in the two regions of the inner Bay of Fundy: Chignecto Bay and Minas Basin. Consistent patterns apparent in the genetic and transcriptomic dataset indicate that Atlantic salmon populations from the inner and outer Bay of Fundy reflect unique genetic lineages, with some evidence of unique genetic legacies between regions of the inner Bay of Fundy, and even between individual rivers within a region. Consistency of the microarray data across two years helps to validate the use of this technique as a useful tool in assessment of variation among wild populations for species conservation. Atlantic salmon samples used in this analysis were collected from Mactaquac and Coldbrook Biodiversity Centres on the east coast of Canada. In year one, eight individuals were hybridized per strain (five strains; 40 individuals in total). This design incorporated dye-swap replicates in which two slides were hybridized with the same pair of individuals, but the dyes were swapped for one of the slides. Therefore, in year one a total of 40 slides were used. Because of the large number of strains assessed in year two (12), dyes were balanced across slides to maximize biological replication. Six individuals were hybridized per strain; three of these were labelled with Cy3, and three were labelled with Cy5 (for a total of 36 arrays in year two).

Dataset Information

Cotton ovule development

Publications

Expression profiling identifies genes expressed early during lint fibre initiation in cotton.

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