title: Illumina HiSeq 2000 paired end sequencing; Transcriptomes and differential gene expression in the Arabidopsis shoot phloem companion cells during flowering
design: Transcriptomes and differential gene expression in the Arabidopsis shoot phloem companion cells during flowering
library_construction_protocol: For each biological replicate, approximately 500 INTACT reporter plants were grown in SDs for 21 days before shifting to LDs. The 0LD, 1LD, 2LD and 3LD samples were collected on the 21st day in SDs and 1, 2, and 3 days after the shift to LD. For each sample, the whole shoot material was collected from approximately 120 seedlings and frozen immediately in Eppendorf tubes suspended in liquid nitrogen.  Plants of the shoot-phloem-companion-cell-tagged  INTACT reporter line (Transgenic SUC2::redNTF and UBQ10::BirA in Col-0 background) were cultivated in growth chambers, in short-day (SD) conditions (8 h light/16 h dark) for 21 days and then shifted to long-day (LD) conditions (16 h light/8 h dark) to induce flowering.  The growth-chamber condition was at 23°C with 65% relative humidity, and with the light at a fluence rate of 125 to 175 μmol m−2 s−1. Total nuclear RNA was extracted from approximately 10,000 nuclei of each sample using the RNeasy Micro Kit (Qiagen). Genomic DNA was removed by DNase I treatment (Thermo Scientific). Double-strand cDNA was synthesized and linearly amplified (Clontech SMARTer Ultra Low Input RNA for Illumina Sequencing-HV kit).  Low Input Library Prep Kit (Clontech) was used for preparation of sequencing libraries
attributes.tag: Experimental Factor: sampling time point
attributes.value: 0