Illumina HiSeq 2000 paired end sequencing; GSM2570302: S0-1; Arabidopsis thaliana; RNA-Seq

S0-1

Arabidopsis plants grown in a hydroponic media with sufficient Nitrogen were given a 60mM supply of Nitrogen. Triplicate sets of plants were sampled at time points 0,5,10,15,20,30,45,60,90 and 120 minutes after supply from treated and control plants (20mM KCl). The samples were flash frozen in liquid N and used to construct RNA-Seq libraries to assay transcriptional changes in the shoots and roots, separately, in response to Nitrogen. Overall design: Time series of shoot and root mRNA profiles from Root and shoot were generated at 10 time points after Nirogen supply using Illumina HiSeq platform.

Fine scale time-series RNA-Seq of shoot and root responses to Nitrogen supply

Submitted by Gene Expression Omnibus on 12-MAY-2018

Approximately 100 mg of tissue was used to extract total RNA from pulverized, frozen roots and shoots with an RNeasy Mini Kit (Qiagen) with on-column DNase treatment. mRNA was purified using Dynabeads Oligo (dT). Reverse transcription was performed using SuperScript III (Invitrogen, 18080-044) with second-strand synthesis with dUTPs, followed by cleanup, end repair, and dA-tailing. Universal Y-shaped adapter ligation was performed to enable sample multiplexing. Library amplification and multiplexing were performed using dUTP excision and amplification followed by PCR enrichment using 2x Phusion HF Master Mix (NEB, M0531L). Size-selection was performed using gel extraction and purification (Qiagen Gel Extraction Kit). Final quantity was determined using the DNA Bioanalyzer Chip and KAPA Library Quant qPCR.

Fine scale time-series RNA-Seq of shoot and root responses to Nitrogen supply

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