title: GSM1213857: Early maturation-stage embryonic axis [RNA-seq]; Glycine max; RNA-Seq
library_construction_protocol: Total RNA was isolated from three seed parts (axis, cotyledon, and seed coat) using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions.  Total RNA was treated with RNase-free DNaseI (Ambion, Austin, TX) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300. Approximately 20 nanogram of total RNA was amplified with Nugen Ovation Pico WTA system v.1 (Nugen, San Carlos, CA).  Double-stranded cDNA was generated using WT-Ovation Exon Module (Nugen, San Carlos, CA) and quantified with Picogreen on the Nanodrop ND-3300 (Nanodrop Technologies).  One microgram of double-stranded cDNA was fragmented using NEB Fragmentase for 15 minutes at 37oC for the standard protocol (NEB, Ipswich, MA).  The Illumina TruSeq DNA Sample prep kit was used to prepare the Illumina library with modifications (Illumina, San Diego, CA).  Specifically, the Covaris shearing step was omitted, the final PCR enrichment step was performed using Agilent Pfu Turbo Cx DNA polymerase (Agilent, Santa Clara, CA) instead of the TruSeq PCR mix, and 12 cycles of PCR were performed. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument. Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing
attributes.tag: GEO Accession
attributes.value: GSM1213857