 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 21, 2019 |
| Title |
strong field embryo sample taken at leaf early stage ST-4 |
| Sample type |
SRA |
| |
|
| Source name |
leaf early
|
| Organism |
Triticum turgidum |
| Characteristics |
genotype: Strong Field (Tetraploid wheat, AABB genome)
tissue: embryo
development stages: leaf early
|
| Treatment protocol |
NA
|
| Growth protocol |
Polyploidy wheats, AC Barrie, Strong Field and diploid wheat grass (DV92) plants were grown in growth chambers under long-day conditions of 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m−2 s−1 for whole life cycle. TA2780 and TA101132 were initially grown in a growth chamber at 22°C under long days (16h day/8h night), at the fifth-leaf stage, plants were moved into a cold room with 4°C and the long day photoperiod for one month (vernalization treatment), then move back to 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m−2 s−1 again to complete its life cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from embryo, endosperm and seed coat of wheat speciesat different development stages following the protocol of RNAqueous-Micro kit (Ambion, Catalog# 1927), two replicates for each development stage. The quantity of RNA isolated from early stage was insufficient for preparation of libraries for the RNA-seq experiments. Therefore the mRNA of all stages was amplified and the aRNA were used for RNA-seq analysis. The mRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750). For RNA-seq profile analysis, we prepared Illumina mRNA-seq libraries using the TruSeq RNA kit (version 1, rev A), the libraries were prepared by using aRNA according to manufacturer's instruction. For HiSeq 2500 sequencing, 4 libraries were pooled per sequencing lane
Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
strong field embryo sample taken at leaf early stage
ST-4
|
| Data processing |
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package FASTX-toolkit [http://hannonlab.cshl.edu/fastx_toolkit/].
RAN-seq reads were aligned to the pan-genome of Chinese Spring (IWGSC RefSeq v1.0) from the IWGSC sequence repository hosted by URGI-INRA (https://wheat-urgi.versailles.inra.fr/) and Fusarium graminearum reference genome (Fusarium graminearum str. PH-1) from EnsemblFungi (http://fungi.ensembl.org/, Release 35) using STAR v2.5.3a
R package DESeq2 was used for data normalization and to generate differentially expressed gene (DEG)
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In excel file format, including raw read counts of each species
|
| |
|
| Submission date |
Apr 11, 2019 |
| Last update date |
Oct 21, 2019 |
| Contact name |
Ziying Liu |
| E-mail(s) |
ziying.liu@nrc-cnrc.gc.ca
|
| Phone |
6139930829
|
| Organization name |
National Research Council, Canada
|
| Street address |
1200 Montreal Road
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1A0R6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL26493 |
| Series (1) |
| GSE129695 |
The Evolution of Gene Expression in Polyploid Wheats and Their Diploid Ancestors during Embryogenesis |
|
| Relations |
| BioSample |
SAMN11400316 |
| SRA |
SRX5671285 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
