Ontology highlight
ABSTRACT:
PROVIDER: PRJNA983862 | ENA |
REPOSITORIES: ENA
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Project description:We describe PolyA-Seq, a strand-specific method for high-throughput sequencing of the 3' ends of polyadenylated transcripts. PolyA-Seq is as accurate for digital gene expression as existing RNA sequencing approaches, and superior to microarrays. We used the approach to map polyadenylation (polyA) sites in 24 samples from normal tissues in human, rhesus, dog, mouse, and rat. Detection of polyA sites in a mixture of 24 tissues in human, mouse, rat, dog and rhesus. Samples included two replicates each of MAQC Human Brain Reference and MAQC Universal Human Reference. Two additional human sets of reads are included that were used to distinguish true polyA sites from internal priming sites.
2011-06-25 | E-GEOD-30198 | biostudies-arrayexpress
Project description:Ras-related associated with diabetes (RRAD) is a small Ras-related GTPase that is frequently inactivated by DNA methylation of the CpG island in its promoter region in cancer tissues. However, the role of the methylation-induced RRAD inactivation in tumorigenesis remains unclear. In this study, the Ras regulated-transcriptome and epigenome were profiled by comparing T29H (a RasV12-transformed human ovarian epithelial cell line) with T29 (an immortalized but non-transformed cell line) through Reduced representation bisulfite sequencing (RRBS-seq) and Digital gene expression (DGE) . We found that RasV12-mediated oncogenic transformation was accompanied by RRAD promoter hypermethylation and a concomitant loss of RRAD expression. In addition, we found that the RRAD promoter was hypermethylated and its transcription was reduced in ovarian cancer versus normal ovarian tissues. Treatment with the DNA methyltransferase inhibitor 5-aza-2M-bM-^@M-2-deoxycytidine (5-aza-dC) resulted in demethylation in RRAD promoter and restored RRAD expression in T29H cells. By employing knockdown and overexpression techniques in T29 and T29H, respectively, we found that RRAD inhibited glucose uptake and lactate production by repressing the expression of glucose transporters. Finally, RRAD overexpression in T29H cells inhibited tumor formation in nude mice, suggesting RRAD is a tumor suppressor gene. Our results indicate that RasV12-mediated oncogenic transformation induces RRAD epigenetic inactivation, which in turn promotes glucose uptake and may contribute to ovarian cancer tumorigenesis Reduced representation bisulfite sequencing (MspI,~40-220bp size fraction) data for two cell lines (T29 and T29H) were generated by deep sequencing, in two replicates, using Illumina HiSeq 2000.
2014-08-21 | E-GEOD-55566 | biostudies-arrayexpress
Project description:High-throughput sequencing of small RNAs from domestic dog lymphocytes Keywords: high-throughput Solexa sequencing
2008-04-07 | GSE10825 | GEO
Project description:High-throughput sequencing of small RNAs from domestic dog lymphocytes Keywords: high-throughput Solexa sequencing Small RNAs were sequenced from domestic dog lymphocytes
2008-04-06 | E-GEOD-10825 | biostudies-arrayexpress
Project description:Purpose: The transcriptome profiles were compared among groups of chronic stress exposure and control in two different breeds to identify genes and pathways related to response to chronic stress in the pituitary-adrenal axis. Methods: 6 male adult CFD and 6 Beagles were chosen at random with the similarities in good health, weight and other aspects. Separately, 3 of these two breeds were freely selected for the stress exposure via intermittent electrical stimulation and restraint stress, while the other 3 of these two breeds were non-disposed for normal control.The details for the disposal of dogs were: every morning dogs were restrained and electrical stimulations were exerted with a stable current of 10 mA for 6 s and then with a 6 s interval, lasting for 20 min every day. The duration of disposal was ten days.ll 12 dogs were killed by air embolism in the 11th day. Subsequently, pituitary and adrenal cortex tissues were fast collected and isolated for further high-sequencing. Results: 8 cDNA libraries were constructed for RNA-seq. A number of reads ranging from 53,295,978 to 65,414,932 was obtained in those 8 groups. About 10,000 genes and transcripts were annotated in each group. Besides,A total of 40, 346, 376, 69, 70, 38, 57, and 71 DEGs were detected in the contrasts of BP1_vs_BP2, CFDP1_vs_CFDP2, BP1_vs_CFDP1, BP2_vs_CFDP2, BAC1_vs_BAC2, CFDAC1_vs_CFDAC2, BAC1_vs_CFDAC1, and BAC2_vs_CFDAC2, respectively. Conclusions: Our results can contribute to a more comprehensive understanding about the genetic mechanisms of response to chronic stress in adrenal cortex and pituitary. Adrenal cortex and pituitary mRNA profiles of adult Chinese Field Dog and Beagle under chronic stress exposure and normal control, including BAC1 (Beagle adrenal cortex with disposal), BAC2 (Beagle adrenal cortex with non-disposal), BP1 (Beagle pituitary with disposal), BP2 (Beagle pituitary with non-disposal), CFDAC1 (Chinese Field Dog adrenal cortex with disposal), CFDAC2 (Chinese Field Dog adrenal cortex with non-disposal), CFDP1 (Chinese Field Dog pituitary with disposal), CFDP2 (Chinese Field Dog pituitary with non-disposal), were generated by deep sequencing, using Illumina Genome Analyzer IIx.
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