PMC:4979054 / 6480-8978 JSONTXT

{"project":"2_test","denotations":[{"id":"27600348-16081474-69481533","span":{"begin":850,"end":852},"obj":"16081474"},{"id":"27600348-10592173-69481534","span":{"begin":1120,"end":1122},"obj":"10592173"}],"text":"2.3. Building the Transcriptome, Custom Design of the Oil Palm Mesocarp Array and Agilent Commercial Array\nA consensus transcriptome sequence was built from reads generated from sequencing oil palm mesocarp tissues collected from samples harvested at different WAA. The reads generated by Roche 454 GS-FLX sequencers were assembled using the Newbler program V2.5 (Roche 454 Life Sciences, Branford, CT, USA). After sequence assembly, sequences shorter than 100 base pairs, as well as those originating from organelles and rRNA, were removed, leaving 31,804 sequences. The sequences have been deposited in the European Nucleotide Archive (ENA) (accession number(s): LM611910–LM643713). In order to undertake a global analysis of the mesocarp gene expression, the transcripts were compared to the Gene Ontology database using BLAST2GO (version 2.3.5) [21]. This process classifies the genes according to the molecular function, biological process or cellular component. Biological pathway analysis of the transcripts was carried out by comparison with plant sequences annotated to reference pathways in the KEGG database [22]. For the processes above, the E-value cutoff for the BLASTx program was set to be 10−5.\nThe custom oil palm mesocarp array probes were designed based on these 31,804 sequences with the annotations obtained by comparing isotig sequences to the Uniprot database [23]. The custom gene expression oil palm mesocarp array was designed using the Agilent eArray web-based application in a 2 × 105K format. Probes were designed using the Agilent internal design program through the eArray website [24]. Each of unique transcriptome sequences was represented by three distinct probes. Agilent 60-mer SurePrint technology was used for array printing.\nIn the cross-species study, the 4 × 44K Arabidopsis (V4) Gene Expression Microarray (G2519F-021169) and the 4 × 44K rice gene expression microarray (G2519F-015241) from Agilent Technologies were used for hybridization with the RNA from the 16 WAA samples. The array consists of 43,803 probes for both Arabidopsis thaliana and rice. The Arabidopsis microarray was designed based on various databases including; NCBI Reference Sequence Database (RefSeq) (July 2008), UniGene (May 2008), TAIR 8 cDNA (April 2008), TIGR (June 2006), TIGR Plant Transcript Assemblies (June 2006) and ATHI (Jan 2004) [25]. The Rice microarray was designed based on resources from National Institute of Agrobiological Sciences, RefSeq and GenBank 2007 [25]."}