Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Peripheral regions and central regions from HT-29 tumors

ABSTRACT: Gene expression of peripheral regions and central regions from HT-29 tumors Sample tissues were immediately frozen by liquid nitrogen after isolation. Total RNAs were extracted from samples with a PureLink RNA Mini Kit (Life Technologies). The integrity of total RNAs was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) was used to prepare Cy3-labelled target cRNA according to the manufacturer's instructions. Labeled cRNAs were hybridized with a SurePrint G3 Human GE 8M-CM-^W60K Microarrays (Agilent Technologies). Three separate hybridizations were performed for each sample. Array images were captured using a DNA Microarray Scanner (Agilent Technologies), and data were analyzed using Feature Extraction Software (Agilent Technologies) to obtain background-corrected signal intensities. Data were further analyzed with GeneSpring GX Software (Version 11.0, Agilent Technologies). After data filtering, mRNAs differentially expressed in target cells versus controls were assessed by FisherM-bM-^@M-^Ys exact test, followed by multiple corrections using the Benjamini and Hochberg false discovery rate (FDR) method. Gene sets with a FDR q-value < 0.05 were considered to be significant.

ORGANISM(S): Homo sapiens

SUBMITTER: Yukie Yoshii

PROVIDER: E-GEOD-64831 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:We examined FASN knockdown LNCaP cells obtained by shRNA transduction with Mission lentiviral transduction particles (SHCLNV-NM 00410, TRCN3128, Sigma) (FASN-RNAi cells). In this study, we used cells transfected with non-targeting shRNA as a control (control-RNAi cells). The expression of genes related to cellular proliferation (phospholipase A2, group IVA, PLA2G4A; tensin 3, TNS3; glypican 4 GPC4), cell adhesion and extracellular matrix organization [peroxidasin homolog (Drosophila) PXDN; sarcoglycan epsilon, SGCE; von Willebrand factor, VWF; hydroxysteroid (17-beta) dehydrogenase 12, HSD17B12; cysteine-rich secretory protein LCCL domain containing 2, CRISPLD2], and cell motility (TNS3, RAP2B member of RAS oncogene family, RAP2B) were shown to be down-regulated by FASN inhibition with RNAi. FASN inhibition led to down-regulation of the PLA2G4A and HSD17B12 genes encoding phospholipase A2 and 17-beta hydroxysteroid dehydrogenase, respectively, which are the key enzymes related to production of an intracellular second messenger arachidonic acid and androgen hormones, both playing roles in promotion of tumor progression. We also found that the genes related to arachidonic acid signalling, including RGS2, SPAG16, VWF and RAP2B, were also suppressed with FASN inhibition. Gene expression profiling therefore demonstrated that FASN inhibition induces down-regulation of genes related to cell proliferation, cell adhesion, migration, and invasion, as well as the production of arachidonic acid and androgen hormones, both of which drive tumor progression. Total RNA isolation was performed with a Micro-to-Midi total RNA purification system (Invitrogen). The integrity of total RNAs was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) was used to prepare Cy3-labelled target cRNA according to the manufacturer's instructions. Labeled cRNAs were hybridized with a SurePrint G3 Human GE 8M-CM-^W60K Microarrays (Agilent Technologies). Two separate hybridizations were performed for each sample. Array images were captured using a DNA Microarray Scanner (Agilent Technologies), and data were analyzed using Feature Extraction Software (Agilent Technologies) to obtain background-corrected signal intensities. The data were further analysed with GeneSpring GX Software (Version 11.0, Agilent Technologies). After filtering of data, mRNAs differentially expressed in target versus control were considered using the Fisher exact test, followed by multiple corrections using the Benjamini and Hochberg false discovery rate (FDR) method. Gene sets with a FDR q-value < 0.05 were considered significant.

Project description:Wild-derived mice have contributed to mouse genetics by their genetic diversity that may increase the chance of identifying novel modifier genes responsible for specific phenotypes and diseases. However, gene-targeting using wild-derived mice has been unsuccessful due to the unavailability of stable embryonic stem cells. Here, we report that the CRISPR/Cas9-mediated gene-targeting can be applied to the Japanese wild-derived MSM/Ms strain. We targeted the nonagouti (a) gene encoding the agouti protein localized in hairs and the brain. We obtained three homozygous knockout mice as founders, all showing black coat color. While homozygous knockout offspring were physiologically indistinguishable from wild-type littermates, they showed specific domesticated behaviors; a high locomotion during the light period and a decline in the avoidance of a human hand. These phenotypes were consistent over the subsequent generations. Our findings support the empirical hypothesis that nonagouti is a domestication gene, which might repress aggressive behavior. Global gene expression patterns in the midbrain of wildtype and nonagouti (a) homogygous mutant MSM/Ms mice were analyzed by one-color Mouse Gene Expression 8x60K microarray. The midbrain tissues were manually isolated from 8-9 weeks old mice under dissecting microscope. Total RNA was purified from dissected midbrain using Trizol (Thermo Fisher Scientific). Purified total RNA was amplified and labeled with Cy3 using Low-Input QuickAmp Labeling Kit (Agilent Technologies). Cy3-labeled RNAs were hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray Kit (Agilent Technologies) at 65 Â°C for 17h. After wash, the hybridized slides were scanned with DNA microarray scanner (Agilent Technologies). The scanned images were processed with Feature Extraction software (Agilent Technologies) to extract signal intensities of each probe. The extracted signal data were imported into the Gene Spring GX 13.1.1 software (Agilent Technologies) and normalized using the default settings. Two and six biological replicates were performed in wildtype and mutant group, respectively.

Project description:We evaluated liver transcriptome throughout gestation and early lactation of purebred and crossbred beef cows (Angus, Hereford and their F1 crossbreeds, CR), grazing high or low herbage allowances (HA) of native grasslands (4 and 2.5 kg DM/kg BW annual mean; n = 16) using an Agilent 4x44k bovine array. A total of 4,661 transcripts were affected by days (272 M-bM-^IM-% 2.5-fold difference, FDR M-bM-^IM-$ 0.10) and 47 pathways were altered during winter gestation (-165 to -15 days relative to calving, d). Gluconeogenesis and fatty acid oxidation pathways were substantially upregulated, while cell growth, DNA replication and transcription pathways were downregulated (FDR M-bM-^IM-$ 0.25). We observed only small changes in the liver transcriptome during the early lactation period (+15 to +60 d). A total of 225 genes were differentially expressed (47 M-bM-^IM-% 2-fold difference, FDR M-bM-^IM-$ 0.10) between HA. The majority of those were related to glucose and pyruvate metabolism and were upregulated in high HA, reflecting their better metabolic status. Two genes were upregulated in CR cows, but 148 transcripts (74 M-bM-^IM-% 2-fold change difference, FDR M-bM-^IM-$ 0.10) were affected by the HA and cow genotype interaction. The transcriptional changes observed indicates a complex and previously unrecognized adaptive program in beef cow liver. We report novel candidate genes, metabolic pathways, and regulatory mechanisms, which can be used as targets of future studies. Complete randomized block design with two spatial replications and a factorial arrangement of herbage allowance (HA) and cow genotype (CG). Herbage allowance treatments represented 4 and 2.5 kg DM/kg BW of annual mean (HI and LO, respectively). Four purebred (PU M-bM-^@M-^S Hereford, H and Angus, A) and four crossbred (CR - F1, HA and AH) multiparous pregnant cows (5 to 6 year-old), were evaluated per treatment (HI-CR, HI-PU, LO-CR, and LO-PU) throughout the gestation and lactation period (-165 to +60 days relative to parturition, days). Cows belonged to or were descendants of experimental animals generated as part of a diallel crossbreeding experiment carried out for 10 years at the Experimental Station and were assigned to the same forage allowance (HI or LO) since May 2007 and gestated and lactated one calf every year from 2007 to 2009.

Dataset Information

Peripheral regions and central regions from HT-29 tumors

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure