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[…] ets with basal flowers at the beginning of anthesis, representing all developmental stages, were collected and total RNA was extracted using a NucleoSpin® miRNA kit (Machery-Nagel, Düren, Germany). Each genotype was represented by two biological replicates. The samples were sequenced using the 454 GS FLX + Roche method at INDEAR (Instituto de Agrobiotecnología de Rosario, Santa Fe, Argentina). Raw reads were deposited in the Sequence Reads Archive (SRA) database at NCBI as BioProject 358210 “Floral transcriptome of sexual and apomictic Eragrostis curvula” including Biosamples SAMN06167423 (reads from OTA-S) and SAMN06167424 (reads from Tanganyika). Curated raw sequences were assembled using Newbler Assembler software v2.6 (Roche, Indianapolis, IN, USA)., Differential expression between two conditions was analyzed using the EdgeR package and P-values adjusted using the Benjamini and Hochberg method to control the false discovery rate. A corrected P-value of 0.01 and log2 (fold-change) of 1 were used as thresholds for significant differential expression., Arabidopsis and maize protein sequences for AtAGO9/ZmAGO104, AtDDM1/ZmCHR106, and AtCMT3/ZmDMT102 were retrieved, respectively, from The Arabidopsis Information Resource (TAIR) and the Maize Genetic and Genomic Database (MaizeGDB), and used to query the 454 RNA libraries using BLASTP. Gene families were aligned using a BLOSUM30 matrix and ClustalW in pairwise alignments (open gap penalty: 10; gap extend penalty: 0.1) and multiple alignments (gap extend penalty: 0.2; delay divergent setting: 30%) were generated. A phylogenetic reconstruction was conducted using a neighbor-joining method in MEGA v6.0. Unrooted consensus trees were obtained from 1000 bootstrap replicates., Flowers from OTA-S (sexual plant) and Tanganyika (apomictic plant) were collected and divided in both archesporial and gametophytic stages (Fig. ). Total RNA was extracted as described above. The RNA was reverse-transcribed using the ImProm-II™ Reverse Transcription System (Promega, Madison, WI, USA). Real-time PCR reactions were conducted as previously, using […]

Pipeline specifications

Software tools Newbler, edgeR, BLASTP, Clustal W
Databases TAIR