4 WT individual mice kidneys versus 5th WT kidney, their littermate
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE1586 | GEO | 2004/07/27
SECONDARY ACCESSION(S): PRJNA90735
REPOSITORIES: GEO
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Project description:Every individual kidney was hybridised 4 times including 2 dye swaps: K1: 23557-23560 K2: 23561-23564 K3: 23565-23568 K4: 23569-23572 Only 2 of 4 hybridisations were made at one sample preparation. Keywords: parallel sample
2004-07-27 | GSE1585 | GEO
Project description:We applied DIA Proteomic Analysis to explore Differentially expressed proteins between WT sperms and Cfap77-KO sperms. In this DIA Proteomic Analysis project, there were 6 Mus_musculus samples named W1,W2,W3,C1,C2,C3 and we did 1 technical duplicate experiments. Totally 94339 peptides and 6525 proteins were identified with 1% FDR. Proteins with 2 fold change (mean value of all comparision groups) and P-value (t-test of all comparision groups) less than 0.05 were defined as differentially expressed proteins.
2024-09-18 | PXD056128 |
Project description:The transcriptome of Blochmannia floridanus, the endosymbiont of the carpenter ant Camponotus floridanus, is presented during eight developmental stages of its holometabolous host by use of a whole genome DNA-macroarray. The detected transcription patterns indicate the presence of local transcription units as well as global regulatory mechanisms. Yet, the overall regulation scale is very modest, rarely exceeding a factor of three which is in line with the low number of transcriptional regulators present in this reduced genome. A large number of genes show differential expression in different life stages and a distinct expression pattern of genes possibly involved in symbiotic function as compared to housekeeping genes is apparent. However, these transcriptional changes are small as compared to the changes in the number of bacteria during host development which is highest in pupae and in young imagines. Control of replication of the bacteria in certain life stages may therefore be the decisive parameter influencing overall gene expression of Blochmannia in the animal. The few highly expressed genes like those encoding molecular chaperones exhibit a significantly higher G+C-content than moderately expressed genes. Keywords: Host stage-dependent gene expression C. floridanus laboratory colonies were maintained under constant conditions at 25°C with a 12 h light cycle in artificial nests and fed twice a week with cockroaches (Nauphoeta cinerea), Bhatkar agar (Bhatkar and Whitcomb, 1970), and honey water (50% wt/wt) ad libitum. Developmental stages were defined as L1 (very young larvae, still clustered), L2 (older larvae, approx. 2-4 mm), P1 (pupae before metamorphosis), P2 (pupae after metamorphosis, still uncolored), P3 (pupae shortly before eclosion with dark abdomens), W1 (workers shortly after eclosion, not completely melanized, no aggressive behavior), W2 (fully melanized adult workers from the nest, age not distinguishable), and W3 (adult workers from isolated subcolonies, at least 4 months old). For RNA preparations, midguts of the respective life stage (L2 - W3) were dissected and bacteria were isolated by homogenization and centrifugation. Endosymbionts from small larvae (L1) were isolated from whole animals. RNA for each cDNA array experiment was isolated from individual bacterial preparations; from L1 to W2, each developmental stage was represented by at least three independent experiments and samples from at least three different ant colonies. Two ant colonies (C79 and C118) were represented in every stage from L1 to W2 with additional samples from six other colonies. Old W3 workers were collected from two isolated subcolonies derived from the same mother colony, each sampled in duplicate.
2008-11-09 | E-GEOD-12148 | biostudies-arrayexpress
Project description:E1,E2,E3,N1,N2,N3,S1,S2,S3,W1,W2,W3 Raw sequence reads
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Project description:To investigate the role of miRNAs in the progression of colon cancer, we performed comprehensive miRMA microarray analysis on RNA derived from colon cancer tissues and normal colon tissues. We identified a novel set of colon cancer-related miRNAs. Total RNA was isolated from colon cancer tissues and normal colon tissues. Six-condition experiment: H normal tiss vs. H tumor tissue, S normal tiss vs. S tumor tissue, W1 normal tiss vs. W1 tumor tissue, M normal tiss vs. M tumor tissue, W2 normal tiss vs. W2 tumor tissue, and Y normal tiss vs. Y tumor tissue. Biological replicates: 1H normal tiss, 1H tumor tissue, 1S normal tissM-oM-<M-^L1S tumor tissue, 1W1 normal tissM-oM-<M-^L1W1 tumor tissue, 1M normal tissM-oM-<M-^L1M tumor tissue, 1W2 normal tissM-oM-<M-^L1W2 tumor tissue, 1Y normal tiss and 1Y tumor tissue, independently grown and harvested. One replicate per array.
2013-12-16 | E-GEOD-53339 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) play important roles in intestinal diseases; however, the role of miRNAs during weaning stress is unknown. In our study, six jejunal small RNA libraries constructed from weaning piglets at 1, 4 and 7 d after weaning (libraries W1, W4 and W7, respectively) and from suckling piglets on the same days as the weaning piglets (libraries S1, S4 and S7, respectively) were sequenced using Solexa high-throughput sequencing technology. Overall, 260 known swine miRNAs and 317 novel candidate miRNA precursors were detected in the six libraries. The results revealed that 16 differentially expressed miRNAs were found between W1 and S1; 98 differentially expressed miRNAs were found between W4 and S4 (ssc-mir-146b had the largest difference and ssc-mir-215 had the highest expression level); and 22 differentially expressed miRNAs were found between W7 and S7. Sequencing miRNA results were validated using RT-qPCR. Approximately 12,819 miRNA-mRNA interactions corresponding to 4,250 target genes were predicted. The biological analyses revealed that the differentially expressed miRNAs regulated small intestinal metabolism, stressful responses, cellular and immune functions and miRNA biosynthesis in piglets. Therefore, the small intestine miRNA transcriptome was significantly different between weaning and suckling piglets; the difference varied with the number of days after weaning.
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Project description:We analysed DNA from two brain regions (cerebellum, CER and frontal cortex, FC) from 4 Parkinson's disease (PD) and 4 control brains on a custom design 8x60k Agilent aCGH targeted to PD genes. All brain DNA samples were hybridised with Agilent sex-matched reference DNA, and three CER samples were hybridised against the FC of the same brain, with a dye swap in one. Male and female reference DNA were hybridised to eachother. The samples were then re-extracted with additional protocols, and hybridisations were performed for two CER samples betwen DNA extracted from the same CER with different protocols, and for one brain between the CER and FC new extraction.
2016-02-01 | GSE71360 | GEO