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Sample GSM5130007 Query DataSets for GSM5130007
Status Public on Jul 26, 2021
Title preembryo stage embryo RNA-seq [PEM-2]
Sample type SRA
 
Source name embryo
Organism Brachypodium distachyon
Characteristics tissue: embryo
developmental stage: preembryo
ecotype: Bd21
Treatment protocol Brachypodium flowers were emasculated and pollinated at the flower stage, to ensure sufficient and developmentally coordinated seed production for embryo isolation.
Growth protocol Plants were grown under 16h of light, 22°C and 8h of dark, 20°C photoperiod 100-120 μE m−2 s−1 light intensity.
Extracted molecule total RNA
Extraction protocol Embryo, endosperm and seed coat isolations were performed using a dissecting microscope, fine forceps and needles in a 4.8% Sucrose solution that contained 0.1% RNALater solution.For seed coat isolation, the embryos were manually removed, and the remaining seed coat was kept. Total RNA was extracted from each stage embryo sample following the protocol of RNAqueous-micro kit.
RNA-seq libraries were prepared using TruSeq RNA kit (version 1, rev A).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description PEM-2
Data processing Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads and eliminating short reads using Trimmomatic.
Salmon was used for fast and accurate alignment of cleaned reads to released JGI v3.1 annotation of B. distachyon Bd21 downloaded from the Phytozome database (http://phytozome.jgi.doe.gov/).
Salmon was used to obtain TPM and CPM of each sample.
Genome_build: B. distachyon Bd21 downloaded from the Phytozome database (http://phytozome.jgi.doe.gov/)
Supplementary_files_format_and_content: Matrix table files include log 2 CPM for each Sample
 
Submission date Mar 03, 2021
Last update date Jul 26, 2021
Contact name Peng Gao
E-mail(s) [email protected]
Organization name Agriculture and Agri-Food Canada
Street address 107 Science Place
City Saskatoon
State/province Saskatchewan
ZIP/Postal code S7N 0X2
Country Canada
 
Platform ID GPL17337
Series (1)
GSE168154 Global gene expression in Brachypodium during embryo development
Relations
BioSample SAMN18127736
SRA SRX10225490

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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