SR3
Brachypodium distachyon
Protocols: For RNA-seq transcriptome analysis, stem tissue from four plants each of WT, SWAM4- OE, SWAM4-DR, swam4-1, and swam4-2 lines were individually taken at the end of heading when inflorescence fully emerged, stage 5-9 BBCH-scale (Hong et al., 2011). Samples were collected at ZT22 during the 4-hour dark cycle. Stem tissue was flash-frozen in liquid nitrogen and ground as described above. B. distachyon accession Bd21-3 was used as genetic background (Vogel and Hill, 2008). Seed was imbibed in water at 4°C for ten days and planted in pots with a mix 3:1 ratio of potting mix (Sun Gro Sunshine #8 / Fafard 2 Mix, Burton, OH) and turface (Pro's choice Sports Field Products, Chicago, IL). Treatment with Gnatrol (Valent Bioscience corporation, Libertyville,IL) was made 24 hours prior to planting. Plants were grown in long day conditions 20-hour light/4-hour dark at 26°C and 18°C respectively in a Conviron growth chamber (Controlled Environments Ltd, Manitoba, Canada) at a fluence rate of 220 μmol m-2 sec-1 and 68% relative humidity. Total RNA was extracted using the RNeasy Plant mini kit (Qiagen) and treated with RNase-Free DNase set (Qiagen). RNA samples were resuspended in 50 μl DEPC-treated water, and RNA concentration was estimated by Qubit RNA BR assay kit (ThermoFisher, life technologies, Waltham, MA) in a Qubit 2.0 fluorometer (Life technologies) following manufacturer's recommendation. Quality assessment of RNA was performed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Lexington, MA). Samples with an RNA integrity number (RIN) above 7.0 were selected for library construction and sequencing. Seventeen mRNA libraries were created by poly A selection and sequenced on the Illumina NovaSeq 6000 system -flow cell type S2 2 x 100bp. Library preparation and sequencing was performed at Yale Center for Genome Analysis (YCGA Yale-West campus, Orange, CT) using the Illumina platform.
ENA-FIRST-PUBLIC
2019-08-02T04:03:02Z
ENA-LAST-UPDATE
2019-07-23T15:32:58Z
External Id
SAMEA5806214
INSDC center name
UMass Amherst
INSDC first public
2019-08-02T04:03:02Z
INSDC last update
2019-07-23T15:32:58Z
INSDC status
public
Submitter Id
E-MTAB-8172:SR3
age
26
broker name
ArrayExpress
common name
stiff brome
cultivar
Bd21
developmental stage
stage 5-9 BBCH-scale
genotype
GNRF overexpression
organism part
stem
sample name
E-MTAB-8172:SR3
scientific_name
Brachypodium distachyon