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Importance in salivary gland development and EBN composition were selected for

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SOAPdenovo-Trans software was used to perform de novo assembly and generated 47,596 (AFC), 55,331 (AFM), 40,330 (AMC), and 44,145 (AA) contigs; the average order 1218778-77-8 contig size exceeded 200 bp for all four libraries (Table 3). The array contained four internal positive control probes and five negative controls for data normalization. Seven housekeeping genes were selected based on expression profile analysis to determine PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28724915 the appropriate thresholds for measuring significant hybridization signals over the background. After pre-processing and normalization, log2-transformed RNA-Seq and nCounter data from 36 genes were compared, and the concordance of the data from both technologies were evaluated.the completeness of the assembled transcript sequences. A total of 142 (57.66 ) Core Eukaryotic Genes (CEGs) were identified as full-length, whereas a total of 185 (74.6 ) core genes were retrieved as partial CEGs (Additional file 4: Table S3).Functional annotation and classification of the assembled UnigenesResultsOverview of the swiftlets' transcriptome landscapeAfter removing the amplification adapters and the ambiguous reads, we generated a total of 17.4 million, 17.7 million, 19.6 million, and 15.1 million clean reads for AFC, AFM, AMC, and AA, respectively PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412 (Table 1). The results showed that 99 of the sequenced reads passed quality control with Phred scores of more than 20, indicating that the error rate of the sequencing process was less than 0.01 . SOAPdenovo-Trans software was used to perform de novo assembly and generated 47,596 (AFC), 55,331 (AFM), 40,330 (AMC), and 44,145 (AA) contigs; the average contig size exceeded 200 bp for all four libraries (Table 3). More than 65 of the reads could be mapped back to the reference transcripts in all four experimental groups. Furthermore, for all four groups, more than 96 of the genes were longer than 100 bp, more than 20 of the genes were 500 to 1000 bp, 11 of the genes were longer than 1000 bp, and 0.01 of the genes for AFC, AFM, and AA exceeded 10 kbp (Table 1). CEGMA analysis was used to analyzeTable 1 Overview of the sequencing and assemblySequencing parameters Contig (n) Contig N50 size Total length of contig Scaffolds (n) Scaffold N50 size Maximum length of scaffold Species and location AFC 47,596 252 AFM 55,331 269 AMC 40,330 256 AA 44,145 244 9,807,398 28,051 1143 15,348The generated, non-redundant, reference transcript was used for gene predictions by AUGUSTUS and a total of 14,835 genes were predicted. The functional annotation of genes was first performed using the BLASTx function in the Blast2GO tool against the non-redundant (NR) protein database from NCBI and the UniProt database with an E-value of