Відмінності між версіями «G exons, rRNA, tRNA, snoRNA, snRNA, and identified miRNAs, we pooled»
(Створена сторінка: We also identified three prospective novel miRNAs regarded as to become [http://www.heb-hjjp.com/comment/html/?.html Ding.Read length 700 700 2x150 2x150 2xRead...) |
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| − | We also identified | + | 3 Expression levels of known miRNA families in CL and DT librariesstress in prior studies: miR156 [31, 61], miR159 [23], miR167 [23, 61], miR395 [62], and miR408 [63]. We also identified 3 potential novel miRNAs viewed as to become drought-response miRNAs depending on the differential expression involving the CL and DT libraries. Of those miRNAs, two (sit-novel-miR10, sit-novelmiR56) were upregulated, and a single ([http://www.medchemexpress.com/BX795.html BX795 web] sit-novel-miR18) was downregulated (Added file 7). To confirm the results of miRNA sequencing and bioinformatics evaluation, six recognized miRNAs (sit-miR159b, sit-miR167b, sit-miR390, sit-miR394, sit-miR396a, and miR408) and 4 novel miRNAs (sit-novel-miR15, sitnovel-miR18, sit-novel-miR53, and sit-novel-miR56) were chosen randomly for validation by qRT-PCR. The outcomes showed that the fold transform of expression obtained by qRT-PCR was not fully consistent with bioinformatics analysis outcomes, but the expression trend was equivalent (Fig. 4). The stem-loop secondary structure of four novel miRNAs is shown in Fig. 5. These benefits suggested that Solexa sequencing was successfully applied to determine drought-related miRNAs in foxtail millet.Table 3 Possible novel miRNAs with miRNA* discovered in S.G exons, rRNA, tRNA, snoRNA, snRNA, and known miRNAs, we pooled the remaining unannotated sRNA sequences of two libraries and predicted novel miRNAs utilizing miRcat computer software with default plant parameters and psRobot application. A total of 72 novelTo determine drought-associated miRNAs of foxtail millet, we removed miRNAs whose expression levels have been also low to be analyzed for differential expression (sequencing frequency [https://dx.doi.org/10.1037/a0022827 title= a0022827] DT libraries) and compared the normalized expression of miRNAs involving the CL and DT libraries. A total of 18 recognized miRNAs belonging to 16 households had been substantially expressed with additional than one log2 fold alter (Further file six). Among these DE miRNAs, 14 miRNAs (sit-miR1432-3p, sit-miR156a-5p, sit-miR156b-5p, sit-miR164a-5p, sit-miR167b-5p, sit-miR 171c-3p, sit-miR2118-3p, sit-miR390-5p, sit-miR394-5p, sit-miR395-3p, sit-miR408-3p, sit-miR529a-3p, sit-miR 529b-3p, and sit-miR827) were upregulated and four miRNAs (sit-miR159b-3p, sit-miR319c-5p, sit-miR528-5p and sit-miR535-5p) had been downregulated; a number of these miRNA households have already been related with droughtTable 2 Statistical evaluation of sRNAs for manage (CL) and drought-treatment (DT) librariesCL (manage) Form Exon antisense Exon sense Intron antisense Intron sense miRNA rRNA repeat tRNA other people Total Uniq sRNAs 137 394 34 225 8698 98782 10278 7782 1361528 1487858 % 0.01 0.03 0.00 0.02 0.58 six.64 0.69 0.52 91.51 one hundred.00 Total sRNA 141 491 35 252 117589 2310754 184428 217892 11292502 14124084 Percent 0.00 0.00 0.00 0.00 0.83 16.36 [https://dx.doi.org/10.1038/srep18714 title= srep18714] 1.31 1.54 79.95 one hundred.00 DT (drought-treatment) Uniq sRNAs 94 180 29 91 7814 118155 10425 9434 1433632 1579854 Percent 0.01 0.01 0.00 0.01 0.49 7.48 0.66 0.60 90.74 100.00 Total sRNA 95 191 29 93 104080 2026243 197797 152753 7893561 10374842 % 0.00 0.00 0.00 0.00 1.00 19.53 1.91 1.47 76.08 one hundred.Wang et al. BMC Genetics (2016) 17:Page six ofTarget prediction of miRNAs and validation by degradome sequencingFig. |
Поточна версія на 09:26, 25 січня 2018
3 Expression levels of known miRNA families in CL and DT librariesstress in prior studies: miR156 [31, 61], miR159 [23], miR167 [23, 61], miR395 [62], and miR408 [63]. We also identified 3 potential novel miRNAs viewed as to become drought-response miRNAs depending on the differential expression involving the CL and DT libraries. Of those miRNAs, two (sit-novel-miR10, sit-novelmiR56) were upregulated, and a single (BX795 web sit-novel-miR18) was downregulated (Added file 7). To confirm the results of miRNA sequencing and bioinformatics evaluation, six recognized miRNAs (sit-miR159b, sit-miR167b, sit-miR390, sit-miR394, sit-miR396a, and miR408) and 4 novel miRNAs (sit-novel-miR15, sitnovel-miR18, sit-novel-miR53, and sit-novel-miR56) were chosen randomly for validation by qRT-PCR. The outcomes showed that the fold transform of expression obtained by qRT-PCR was not fully consistent with bioinformatics analysis outcomes, but the expression trend was equivalent (Fig. 4). The stem-loop secondary structure of four novel miRNAs is shown in Fig. 5. These benefits suggested that Solexa sequencing was successfully applied to determine drought-related miRNAs in foxtail millet.Table 3 Possible novel miRNAs with miRNA* discovered in S.G exons, rRNA, tRNA, snoRNA, snRNA, and known miRNAs, we pooled the remaining unannotated sRNA sequences of two libraries and predicted novel miRNAs utilizing miRcat computer software with default plant parameters and psRobot application. A total of 72 novelTo determine drought-associated miRNAs of foxtail millet, we removed miRNAs whose expression levels have been also low to be analyzed for differential expression (sequencing frequency title= a0022827 DT libraries) and compared the normalized expression of miRNAs involving the CL and DT libraries. A total of 18 recognized miRNAs belonging to 16 households had been substantially expressed with additional than one log2 fold alter (Further file six). Among these DE miRNAs, 14 miRNAs (sit-miR1432-3p, sit-miR156a-5p, sit-miR156b-5p, sit-miR164a-5p, sit-miR167b-5p, sit-miR 171c-3p, sit-miR2118-3p, sit-miR390-5p, sit-miR394-5p, sit-miR395-3p, sit-miR408-3p, sit-miR529a-3p, sit-miR 529b-3p, and sit-miR827) were upregulated and four miRNAs (sit-miR159b-3p, sit-miR319c-5p, sit-miR528-5p and sit-miR535-5p) had been downregulated; a number of these miRNA households have already been related with droughtTable 2 Statistical evaluation of sRNAs for manage (CL) and drought-treatment (DT) librariesCL (manage) Form Exon antisense Exon sense Intron antisense Intron sense miRNA rRNA repeat tRNA other people Total Uniq sRNAs 137 394 34 225 8698 98782 10278 7782 1361528 1487858 % 0.01 0.03 0.00 0.02 0.58 six.64 0.69 0.52 91.51 one hundred.00 Total sRNA 141 491 35 252 117589 2310754 184428 217892 11292502 14124084 Percent 0.00 0.00 0.00 0.00 0.83 16.36 title= srep18714 1.31 1.54 79.95 one hundred.00 DT (drought-treatment) Uniq sRNAs 94 180 29 91 7814 118155 10425 9434 1433632 1579854 Percent 0.01 0.01 0.00 0.01 0.49 7.48 0.66 0.60 90.74 100.00 Total sRNA 95 191 29 93 104080 2026243 197797 152753 7893561 10374842 % 0.00 0.00 0.00 0.00 1.00 19.53 1.91 1.47 76.08 one hundred.Wang et al. BMC Genetics (2016) 17:Page six ofTarget prediction of miRNAs and validation by degradome sequencingFig.
