Illumina HiSeq 2000 paired end sequencing; Transcriptional responses ... - SRA

ERX1813797: Illumina HiSeq 2000 paired end sequencing; Transcriptional responses to cold in five Pooideae species
1 ILLUMINA (Illumina HiSeq 2000) run: 18.2M spots, 4.6G bases, 2.1Gb downloads

Design: Transcriptional responses to cold in five Pooideae species

Submitted by: Department of Chemistry, Biotechnology and Food Science (IKBM), Norwegian University of Life Sciences (NMBU), NORWAY (Department of Chemistry, Biotechnology and Food Sc)

Study: Transcriptional responses to cold in five Pooideae species

PRJEB18276 • ERP020203 • All experiments • All runs

show Abstracthide Abstract

To investigate the evolution of cold response in Pooideae, five species spanning early to later diverging lineages were sampled before and after subjecting them to a drop in temperature (17°C to 6°C), shorter days (12 to 8 hours of light) and less intensive light. Short-term response was sampled in the afternoon 8 hours after drop in temperature but 24 hours after the respective control sample to control for diurnal rhythm. Long-term response was sampled after 4 and 9 weeks in the morning directly after lights were turned on with a respective control sample also taken in the morning on the day before the temperature drop.

Sample: HoVu.W0.mix.1

SAMEA18181918 • ERS1462357 • All experiments • All runs

Organism: Hordeum vulgare

Library:

Name: HoVu.W0.mix.1_p

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: unspecified

Layout: PAIRED

Construction protocol: Leaf material was collected and flash frozen i) in the afternoon (8 hours after lights on) before cold treatment and the next day 8 hours after cold treatment and ii) in the morning (at lights on) before cold treatment, 4 weeks after cold treatment and 9 weeks after cold treatment. Seeds were germinated and initially grown in a greenhouse at a neutral day length (12 hours of light), 17°C and a minimum artificial light intensity of 150 µmol/m2s. Depending on the species, one to eight week old plants were randomized and distributed to two cold chambers with short day (8 hours of light), 6°C and a light intensity of 50 µmol/m2s. Cold (6°C) with short day (8 hours of light), and a light intensity of 50 µmol/m2s. Flash frozen leaves were individually homogenized using a TissueLyser (Qiagen Retsch) and total RNA was isolated (from each leaf) using RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions. The purity and integrity of total RNA extracts was determined using a NanoDrop 8000 UV-Vis Spectrophotometer (Thermo Scientific) and 2100 Bioanalyzer (Agilent), respectively. Strand-specific TruSeq RNA-seq library prep (Illumina)

Spot descriptor:

1 forward127 reverse

Experiment attributes: (show all 6 attributes...) (hide...)

Experimental Factor: Hordeum vulgare: organism

Experimental Factor: 17: temperature

Experimental Factor: 12: day length

Experimental Factor: 150: light intensity

Experimental Factor: 0: sampling time after light on

Experimental Factor: control: sampling time point

Runs: 1 run, 18.2M spots, 4.6G bases, 2.1Gb

Run	# of Spots	# of Bases	Size	Published
ERR1744566	18,194,235	4.6G	2.1Gb	2016-12-13

ID:: 3512783

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