Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Solexa sequencing of small RNAs in Sprague-Dawley (SD) rat [proximal sciatic nerve]

ABSTRACT: We applied Solexa sequencing technology to identify rat microRNA genes in proximal sciatic nerve following sciatic nerve resection. Using Solexa sequencing, computational analysis and Q-PCR verification, 93 novel miRNAs in rats were discovered and identified, of which 42 novel miRNAs were first reported in proximal sciatic nerve of rat and 51 novel miRNAs were produced at days 1, 4, 7 and 14 after sciatic nerve resection. These data provide an important resource relating to the role and regulation of miRNAs for future studies relating to peripheral nerve injury and regeneration. Keywords: Small RNA sequencing 18-30 nt small RNAs from proximal sciatic nerve of 30 Thirty Sprague-Dawley (SD) rats were sequenced at one Solexa lane

ORGANISM(S): Rattus norvegicus

SUBMITTER: xiaosong gu

PROVIDER: E-GEOD-26753 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background. The lack of noninvasive biomarkers of rejection remains a challenge in the accurate monitoring of deeply buried nerve allografts and precludes optimization of therapeutic intervention. This study aimed to establish the expression profile of circulating microRNAs (miRNAs) during nerve allotransplantation with or without immunosuppression. Methods. Balb/c mice were randomized into 3 experimental groups, that is, (1) untreated isograft (Balb/c M-bM-^FM-^R Balb/c), (2) untreated allograft (C57BL/6 M-bM-^FM-^R Balb/c), and (3) allograft (C57BL/6 M-bM-^FM-^R Balb/c) with FK506 immunosuppression. A 1-cm Balb/c or C57BL/6 donor sciatic nerve graft was transplanted into sciatic nerve gaps created in recipient mice. At 1, 3, 7, 10, and 14 d after nerve transplantation, nerve grafts, whole blood, and sera were obtained for miRNA expression analysis with an miRNA array and subsequent validation with quantitative PCR. Male Balb/c and C57BL/6 mice (age, 10M-bM-^@M-^S12 weeks; weight, 30M-bM-^@M-^S35 g) were purchased from BioLasco (Yi-Lan, Taiwan). The Balb/c mice were randomized into 3 experimental groups: (1) untreated isograft, (2) untreated allograft, and (3) allograft with FK506 treatment. Additional Balb/c and C57BL/6 mice served as sciatic nerve isograft and allograft donors, respectively. These species of mice were selected on the basis of disparity at the MHC locus and prior experience with reciprocal rejection of grafts between these murine strains. FK506 was administered subcutaneously at 1 mg/(kgM-bM-^@M-"d) throughout the experimental course, unless indicated otherwise. At 1, 3, 7, 10, and 14 d after initial surgery (n = 6 animals per group at each time point), sciatic nerve grafts were harvested, and whole blood samples were obtained. Additional sham-operated mice were subjected to the same procedure, including opening of the skin and muscle layers and exposing the sciatic nerve, but without nerve transection or nerve grafting, to measure the effect of FK506 injection on the expression of circulating miRNA. To test the effect of the discontinuation of FK506 treatment on the expression of circulating miRNA, whole blood was drawn at 0, 2, 4, and 6 d after discontinuation of FK506 injection in an additional group of mice with allografts and immunosuppression for 7 d. The whole blood samples (1 mL per mouse) were collected at the indicated times in tubes containing anticoagulant. After the whole blood samples were incubated at room temperature for 15 min, they were centrifuged at 3000 rpm for 10 min, white blood cells were slowly removed from the corresponding layers, and the serum was extracted and stored at M-bM-^@M-^S80M-BM-0C before processing for RNA analyses. All the housing conditions and the surgical procedures, analgesia, and assessments were in accordance with national and institutional guidelines, and an Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC)M-bM-^@M-^Saccredited SPF facility was used. The animal protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of Kaohsiung Chang Gung Memorial Hospital.

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Solexa sequencing of small RNAs in Sprague-Dawley (SD) rat [proximal sciatic nerve]

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