Polymorphism Identification and Improved Genome Annotation of Brassica rapa through Deep RNA Sequencing

Supporting Information for Devisetty et al., 2014

Files in this Data Supplement:

• Supporting Information - Tables S1-S5 and Files S1-S11 (PDF, 234 KB)
• Table S1 - List of primers used to validate SNPs between R500/IMB211 genotypes of B. rapa. (PDF, 174 KB)
• Table S2 - List of primers used for semi-quantitative RT-PCR validations. (PDF, 143 KB)
• Table S3 - Accession numbers of the read sequences submitted to NCBI SRA. (PDF, 166 KB)
• Table S4 - In-silico validation of novel transcripts generated using de novo and reference based assemblies and annotation. (PDF, 197 KB)
• Table S5 - In-silico validation of PASA updated transcript annotations. (PDF, 197 KB)
• FileS1.gz - R500 vs. IMB211 vcf file (.gz, 4.9 MB)
• FileS10.zip - In-silico RNA-Seq coverage and genome annotation validation of novel B. rapa transcripts (IGV screen shots) (.zip, 3.6 MB)
• FileS11.txt - B. rapa GO annotations (.txt, 2 MB)
• FileS2.gz - R500 vs. Chiifu vcf file (.gz, 7 MB)
• FileS3.gz - IMB211 vs. Chiifu vcf file (.gz, 6.5 MB)
• FileS4.zip - B. rapa Chiifu final CDS in fasta format (.zip, 19.9 MB)
• FileS5.fa.zip - B. rapa Chiifu unanchored transcript sequences in fasta format (.zip, 120 KB)
• FileS6.txt - B. rapa Chiifu unanchored transcript sequences gene descriptions (.txt, 134KB)
• FileS7.zip - In-silico RNA-Seq coverage and genome annotation validation of PASA updated B. rapa transcripts (IGV screen shots) (.zip, 4 MB)
• FileS8.txt - B. rapa Chiifu annotation file in bed format (.txt, 4.3 MB)
• FileS9.txt - B. rapa Chiifu transcript sequences gene descriptions (.txt, 2.1 MB)