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Pipeline publication

[…] on 15 July 2015 at 9 AM and from Clayton on 10 July 2015 at 9 AM. RNA was isolated using the Qiagen plant RNeasy isolation kit (Qiagen, Redwood City, CA) with on-column DNAse digestion. RNA quality was validated in a 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). TruSeq RNA libraries from four replicates of each parent and F1 hybrid were sequenced by HiSeq (Illumina, San Diego, CA). After removing primer sequences and low quality sequences with a Phred score less than 34, between 11 million and 32 million high quality sequences remained. shows the number of high quality sequences for each sample. The high quality RNA sequences were aligned to the reference genome (Wm82.a2) using TopHat and the number of sequences that align to the reference genome are shown in []. Gene expression was analyzed using the Cuffdiff 2 program []. Differential expression files and raw sequence files are available from the Gene Expression Omnibus (GSE86608)., Information for the sequence and alignment information including, the sample names, a description of the samples, the total number of sequences after trimming, the number of sequences that aligned to the reference genome and the percent of sequences that aligned to the reference genome., The alignments to the reference sequence were also used to generate variant call files using mpileup. Sequences 2 bp either side of splice junctions were omitted because they have a higher chance of misalignment. Parent specific SNPs were identified that were present in all parental plots sequenced at CRS and their presence in all appropriate parental sequences from CCRS was confirmed. SNPs unique to each parent were identified to generate a list of high quality SNPs specific to each parent. Next, reads that over-lapped these parent-specific SNPs were identified in each F1 hybrid sequenced and the read depths (number of reads) were recorded from each F1 sample sequenced. The F1 hybrids contain one copy of each parental SNP and there was considered to be an allele bias if one allele […]

Pipeline specifications

Software tools TopHat, Cufflinks, SAMtools
Databases GEO