|
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 |