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Pipeline publication

[…] containing poly-N, 5′ adapter contaminants, and poly- A or T or G or C were filtered out with NGQC(Novogene), together with those without a 3′ adapter or insert tag, and reads with low quality scores. Clean reads after filtering accounted for about 97% of the total raw reads (Table ). We selected clean reads with length 18–35 nt for subsequent analysis. The length distribution of this subset peaked at 22 nt (Fig. ). The Pearson correlation between the two individuals in each group was up to 0.96 as calculated from miRNA-seq data, indicating a high concordance rate. The small RNA tags were mapped to the sheep reference genome (ftp://ftp.ensembl.org/pub/release-76/fasta/ovis_aries/dna) using Bowtie [] with no mismatches permitted, and the locations were used to identify known miRNAs. Novel miRNAs were predicted using the applications miREvo [] and mirdeep2 []. Two hundred and thirty two unique miRNAs including 141 conserved miRNAs and 91 novel miRNAs were identified and assigned to genomic coordinates (Additional file  Table S1).Table 1Fig. 1, Hairpin structures of the partial novel miRNA precursors are shown in Additional file  Figure S1. MiRNAs are found on all 26 autosomes and chromosome X (Fig. ), with marked differences in numbers among linkage groups. Although the distribution of miRNAs is highly similar in lambs and adults, miRNA expression differs between the two groups in chromosome 1, 2, 4, 5, 11, 15, 18 and 19.Fig. 2, In order to identify DE miRNAs, we compared the expression of miRNAs between the two lambs and two adults u […]

Pipeline specifications

Software tools Bowtie, miREvo, miRDeep
Organisms Ovis aries, Homo sapiens
Chemicals Steroids