Malawi Duplication 20091207
Ontology highlight
ABSTRACT:
ORGANISM(S): Rhamphochromis sp. 'chilingali'
SUBMITTER: Renn Suzy
PROVIDER: E-GEOD-19368 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:D. yakuba, D. simulans, and D. melanogaster female gDNA hybridized with D. melanogaster male gDNA to assess aCGH as a means of identification of duplicated genes 6 D. melanogaster female vs D. melanogaster male hybs, 6 D. simulans female vs D. melanogaster male hybs, and 4 D. yakuba female vs D. melanogaster male hybs, all with balanced dye swaps
2010-05-16 | E-GEOD-19584 | biostudies-arrayexpress
Project description:Whole brain gene expression profiling for Julidochromis transcriptus male vs. female and Julidochromis marlieri male vs female to identify sex-role biased and sex biased gene expression in these species that exhibit conventional and reversed sex-biased behavior respectively. 5 J. transcriptus male vs. female and 5 J. transcriptus female vs. male hybridizations compare 4 males and 4 females in a balanced loop design with dye-swaps that is independent of the 5 J. marlieri male vs. female and 5 J. marlieri female vs. male hybridizations compare 4 males and 4 females also in a balanced loop design with dye swaps.
2010-07-24 | E-GEOD-23094 | biostudies-arrayexpress
Project description:D. yakuba, D. simulans, and D. sechellia gDNA competitively hybridized against D. melanogaster to evaluate aCGH as a means to identify diverged orthologs. 2 D. sechellia vs D. melanogaster hybs - with dye swap, 2 D. simulans vs D. melanogaster hybs with dye swap, and 8 D. yakuba vs D. melanogaster hybs with balanced dye swaps. D. yakuba vs. D. melanogaster were then analyzed in all 2,4,6,8 possible combinations that incorporated dye-swap to asses sources of variation.
2010-06-21 | E-GEOD-18416 | biostudies-arrayexpress
Project description:We compared RNA samples extracted from spinal cords of control (C) and AT-EAE (E) mice using the "Multiple Yellow" strategy. 4 distinct C-extracts were hybridized with two slides and 4 distinct E-extracts with other two slides, and the green/red normalized signals were compared separately and the E/C ratios averaged. Keywords = white matter Keywords = inflammation Keywords = cDNA microarray Keywords = experimental autoimmune encephalomyelitis
2010-06-10 | E-GEOD-2446 | biostudies-arrayexpress
Project description:Cy3-labeled cDNA from brains of neonatal C57BL Cx43 null, Cx43 heterozygous and Cx32 null mice were compared among themselves and to Cy3-labeled cDNA from brains of neonatal C57BL wildtype mice through Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
2010-06-05 | E-GEOD-1954 | biostudies-arrayexpress
Project description:Cy3-labeled cDNA obtained from four pools of three hearts of neonatal C57BL Cx43 null mice were compared to Cy3-labeled cDNA obtained from four pools of three hearts of neonatal C57BL wildtype mice through Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice. Keywords = Cx32 null vs wildtype neonatal mouse heart
2010-06-05 | E-GEOD-1961 | biostudies-arrayexpress
Project description:miRNA expression was compared in skin from control newborn mice and littermate mice ectopically expressing the potent secreted WNT inhibitor Dickkopf 1 (DKK1) in the epidermis. DKK1 completely suppresses hair follicle development. Multiple miRNAs were identified that reproducibly produced signals above background in both types of skin sample. Several miRNAs were identified for which hybridization signals were on average more than 2.5 fold higher in control samples than in Dkk1-expressing samples, suggesting these may be upregulated in hair follicles, and/or are direct or indirect targets of WNT inhibition in the skin. Keywords: miRNA expression array, transgenic mouse, skin, WNT Low molecular weight RNA was isolated using the mirVana RNA extraction kit (Ambion) from full thickness dorsal skin of three K5-rtTA; tetO-Dkk1 newborn mice and three control littermates following doxycycline treatment from E0.5 to induce expression of Dkk1 in double transgenic epidermis [1]. Control and Dkk1âexpressing transgenic samples were tagged for labeling with Cy3 and Cy5 dyes respectively using the Ncode miRNA Labeling System (Invitrogen), mixed by equal mass, and co-hybridized to miRNA arrays that have been described previously [2]. Background-corrected median signals for pixels from each probe spot in both the Cy3 and Cy5 channels were used for analysis. Cy3 (control samples C2, C4, C5) was detected at 532nm and Cy5 (Dkk1âexpressing transgenic samples TG1, TG2, TG4) at 635 nm. References: [1] Chu, E.Y., Hens, J., Andl, T., Kairo, A., Yamaguchi, T.P., Brisken, C., Glick, A., Wysolmerski, J.J., and Millar, S.E. (2004). Canonical WNT signaling promotes mammary placode development and is essential for initiation of mammary gland morphogenesis. Development 131, 4819-4829. [2] Nelson, P.T., Baldwin, D.A., Scearce, L.M., Oberholtzer, J.C., Tobias, J.W., and Mourelatos, Z. (2004). Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 1, 155-161.
2010-06-11 | E-GEOD-4723 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small regulatory RNAs, which serve fundamental biological roles across eukaryotic species. We describe a novel method for high throughput miRNA detection. The technique is termed RNA-primed, Array-based, Klenow Enzyme (RAKE) assay, because it involves on-slide application of the Klenow fragment of DNA polymerase to extend unmodified miRNAs hybridized to immobilized DNA probes. We used RAKE to study human cell lines and brain tumors. We show that the RAKE assay is sensitive and specific for miRNAs and is ideally suited for rapid expression profiling of all known miRNAs. RAKE offers unique advantages for specificity over Northern blots or other microarray-based expression profiling platforms. Furthermore, we demonstrate that miRNAs can be isolated and profiled from formalinfixed paraffin-embedded tissue, which opens up new opportunities for analyses of small RNAs from archival human tissue. The RAKE assay is theoretically versatile and may be used for other applications, such as viral gene profiling. Keywords = microRNA Keywords: ordered
2010-06-05 | E-GEOD-1821 | biostudies-arrayexpress
Project description:In order to study the function of the Campylobacter jejuni Cj1501 gene, a series of experiments were carried out. Three strains were constructed: a Cj1501 knockout strain, a strain where the Cj1501 knockout was complemented in trans, and a strain with a second copy over-expressing Cj1501 from an fdxA promoter. The transcriptomes of these were all compared to the wild-type strain. The arrays are all from RNA isolated in mid-exponential growth from independent biological replicates. Batch cultures of Campylobacter jejuni NCTC 11168 were grown in 50 ml volumes of Brucella broth in 70cm tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5% Oxygen, 10% Carbon dioxide, 85% Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 M-BM-:C. RNA was extracted from C. jejuni cultures grown to an OD600 of approximately 0.4. Briefly, 0.1 volume of 5% phenol in ethanol was mixed with the broth culture, and after centrifugation RNA was isolated with Tri Reagent (Sigma) and chloroform. RNA was further purified using the RNeasy kit (Qiagen) according to the manufacturerM-bM-^@M-^Ys instructions. The RNA was treated with Turbo DNA-free (Ambion) to remove any residual DNA according to the manufacturerM-bM-^@M-^Ys instructions. RNA concentration was determined using the Nanodrop Spectrophotometer NS-1000 (Thermo Scientific). Two or three independent RNA preparations (biological replicates) of each sample type were labelled and hybridized to custom-designed Agilent microarrays. Equal quantities of RNA from test and control cultures were labelled by using nucleotide homologues of dUTP containing either Cy3 or Cy5 fluorescent dye (Perkin Elmer). For each microarray slide, the test strain was labelled with Cy3-dUTP, while the wild-type sample was labelled with Cy5-dUTP. RNA (15 M-BM-5g) was primed with 5 M-BM-5g pd(N)6 random hexamers (Amersham Biosciences). The Affinity Script kit (GE Healthcare) was used to produce cDNA, and hybridized (Agilent Hi-RPM Gene Expression Hybridization Kit) to the microarray slide according to the manufacturerM-bM-^@M-^Ys instructions. Microarrays were scanned at 5 M-BM-5m using an Axon 4000A scanner, and images were acquired using GenePix Pro 3.0 software (Axon). Related analysis reference: Holmes K., Mulholland F., Pearson B. M., Pin C., McNicholl-Kennedy J., Ketley J. M., Wells J. M. (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur Microbiology-SGM 151 243-257 (PMID 15632442).
2012-07-01 | E-GEOD-35016 | biostudies-arrayexpress
Project description:Whole-genome screening of CpG Island methylation status by array-based profiling of absolute methylation status (array-PAMS). Methylation-specifically digested DNA (Cy3) was hybridized against methylation-sensitively digested DNA (Cy5) from the same sample. CGI methylation in 20 pediatric medulloblastomas (M) and normal cerebellum (Cb, pool of five unaffected donors, age 25â33 years)
2010-06-30 | E-GEOD-4857 | biostudies-arrayexpress