8 protocols
AccessionType
 
feature_extraction
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol and base calling was performed with the Illumina version SCS2.6 software. For the Real Time Analysis (RTA) that is implemented in the SCS control software, we used per lane parameters for basecalling. Barcode splitting was performed as described by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13. Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with tophat 1.3.1 and cufflinks 0.9.2. Genome_build: TAIR9 (available from The Arabidopsis Information Resource) Supplementary_files_format_and_content: A single tab-delimited text file per sample with gene ids and FPKM values.
grow
Plants were grown in Percival AR66L growth chambers under 16 hours of light and 8 hours of dark. Floral buds were collected at stage 12 for RNA preparation. The floral tissue collection methods are as reported by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
nucleic acid library construction protocol
Tissue was frozen in liquid nitrogen, ground to a fine power in liquid nitrogen, and RNA was extracted with the Plant Reagent (Invitrogen using the manufacturer's recommendations). Specific details are as given in Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13. Illumina non-strand-specific (a minor adaptation of the Illumina mRNA-seq methods as reported by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13).
feature_extraction
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol and base calling was performed with the Illumina version SCS2.6 software. For the Real Time Analysis (RTA) that is implemented in the SCS control software, we used per lane parameters for basecalling. Barcode splitting was performed as described by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13. Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with tophat 1.3.1 and cufflinks 0.9.2. Genome_build: Alyrata_107 ('Alyrata_107.fa', which is the nucleotide FASTA format file of the genomic assembly, and 'Alyrata_107_cds.fa', which is the nucleotide FASTA format file of all gene-coding sequences, were downloaded from Phytozome at http://www.phytozome.net/ ). This genome build is as published by Hu et al. 2011. Nat. Genet. 43(5):476-81. Supplementary_files_format_and_content: A single tab-delimited text file per sample with gene ids and FPKM values.
grow
Standardized greenhouse conditions
nucleic acid library construction protocol
Qiagen Rneasy Plant Mini kit, standard protocol Standard Illumina paired-end mRNA seq
feature_extraction
Illumina flourescence data was processed through the illumina analysis Pipeline for basecalling and quality assignment For flowerbud samples, illumina fastq quality scores were converted to PHRED+33, leaf samples were retained at the PHRED+64 format Reads were aligned to the Capsella reference genome using bowtie. The initial release JGI Maker gene models were used to assign expresion using the tophat-cufflinks pipeline including the data normalization option to generate expression FPKM: fragments per Kilobase of exon per million reads. Genome_build: Capsella Rubella v1 (also listed as 183), http://www.phytozome.org/dataUsagePolicy.php?org=Org_Crubella Supplementary_files_format_and_content: TAB delimitted single sample FPKM expression reads, gene models are descibed here ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Crubella/annotation/Crubella_183_gene.gff3.gz