title: GSM1177812: BXM 0DAP; Zea mays; RNA-Seq
library_construction_protocol: The total RNA was isolated from the 36 (12 samples × 3 replicates) groups of plant material using the SDS-Phenol method (Shirzadegan et al., 1991) with the following modification: ~1 g of tissue was ground to a fine powder in liquid nitrogen and homogenized with 6 ml of SDS buffer containing 1% SDS, 50 mMTris-Cl (pH8.0), 150 mMLiCl, 5 mM EDTA (pH 8.0), and 10 mM DTT. The homogenate was mixed with 6 ml phenol:chloroform (5:1, pH4.5, Ambion AM9720) and incubated on ice for 5 min. The mixture was transferred to a 50 ml Phase-Lock-Gel (PLG) tube (5 Prime) and centrifuged at 5,000 rpm (SS-34 rotor) for 10 min at 4°C. The aqueous phase was transferred to a new 50 ml PLG tube. The previous step was repeated with phenol:chloroform (1:1) and chloroform alone. The RNA pellet was precipitated with a 2.5 M LiCl on ice for overnight and washed with ice-cold 2M LiCl. The pellet was then dissolved in TE and mixed with a 1/9 volume of 3 M NaAC (pH5.2) and 2.5 volume of ethanol. The mixture was incubated in a -80°C freezer for at least 4 h. The RNA was pelleted by centrifuge at 14,000 rpm for 15 min at 4°C. After rinsing with 75% ethanol and air-drying, the RNA was dissolved in diethylpyrocarbonate-treated water. The genomic DNA was removed by TURBO DNase I (Ambion) and purified using an RNeasy column (Qiagen). RNA libraries were prepared for sequencing using standard Illumina protocols