Brachypodium distachyon
Protocols: the currently emerging leaf was sampled from at least 3 separate plants, pooled, frozen in liquid nitrogen, then ground to a fine powder. 13 additional time points were collected following this first sample (total 14 time points), one every 3.5 hours. Peeled Brachypodium distachyon Bd21 seeds were sterilized by shaking in 70% ethanol for 5 minutes, followed by shaking in a 50% bleach/0.1% Triton-X100 mixture for an additional 5 minutes. Seeds were then rinsed in sterile water 3 times, stratified at 4 °C for 7 days, then sown (embryo-side down, penetrating the surface) into 100 mL 1x MS + 1% Agar in Magenta Boxes (Caisson Labs, Smithfield, UT). Seeds were germinated in the dark for 3 days, then transferred to diurnal conditions for 10 days (12 hr light, 12 hr dark, 2 °C day temp, 12 °C night temp). Seedlings were then released into one of four conditions: LDHC (12 hr light, 12 hr dark, 28 °C), LDHH (12 hr light, 12 hr dark, continuous 28 °C), LLHC (continuous light, 12 hr 28 °C, 12 hr 12 °C), or LLHH (continuous light, continuous 28 °C). Light intensity was approximately 50 µmol·m-2·sec-1. 12 hours after placing the samples in each condition (the evening of the 10th day, just prior to the anticipated day/night transition). otal RNA was extracted from each sample using the Qiagen RNeasy Plant RNA Extraction Kit (Qiagen, Inc., Hilden, Germany) following the manufacturer's recommended protocol. mRNA was enriched through two rounds of polyA selection using the Dynabeads mRNA Purification kit (ThermoFisher Scientific, Waltham, MA) according to the manufacturer's instructions. Illumina stranded, paired-end sequencing libraries were then constructed using the ScriptSeq-v2 RNA-Seq Library Preparation Kit (Illumina Inc., San Diego, CA) following the manufacturer's instructions.
ENA-FIRST-PUBLIC
2019-05-19T04:02:35Z
ENA-LAST-UPDATE
2019-05-09T10:01:52Z
External Id
SAMEA5599523
INSDC center name
The University of Massachusetts Amherst, MCB program
INSDC first public
2019-05-19T04:02:35Z
INSDC last update
2019-05-09T10:01:52Z
INSDC status
public
Submitter Id
E-MTAB-7950:LLHC6
age
13
broker name
ArrayExpress
common name
stiff brome
developmental stage
BBCH 1.2 (two fully emerged leaves, with one leaf emerging)
ecotype
Bd21
genotype
wild type genotype
growth condition
LLHC (thermocycle,12h:12h, Hot:28C, Cold:12C, constant light)
organism part
leaf
sample name
E-MTAB-7950:LLHC6
sampling site
currently emerging leaf (3rd leaf)
scientific_name
Brachypodium distachyon