|
| Status |
Public on Aug 14, 2018 |
| Title |
M-ES2 |
| Sample type |
SRA |
| |
|
| Source name |
Grain
|
| Organism |
Triticum aestivum |
| Characteristics |
cultivar: Zhou 8425B
tissue: Endosperm (including episperm and pericarp)
developmental stage: 25 day post anthesis
|
| Treatment protocol |
No
|
| Growth protocol |
Wheat (Triticum aestivum L.) cultivar Zhou 8425B were field cultivated at Beijing during cropping seasons.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryo or endosperm (0.2g) were grinned under liquid nitrogen to fine powder using cooled mortar and pestle. Samples were placed in 2ml Eppendorf tubes and total RNA was isolated following the protocol of Plant Total RNA Purification Kit (GMbiolab co., Ltd. Taichung, Taiwan).
The twelve RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Endosperm tissues were collected from 25 DPA
|
| Data processing |
The raw paired reads were trimmed and quality controlled by Seqprep (https://github.com/jstjohn/SeqPrep ) and Sickle (https://github.com/najoshi/sickle ) with default parameters.
The clean reads were aligned to Chinese Spring genome (TGACv1, ftp: //ftp.ensemblgenomes.org/pub/plants/release-36/fasta/triticum_aestivum; Gff3: ftp://ftp.ensemblgenomes.org/pub/plants/release-36/gff3/triticum_aestivum/) using TopHat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009
Differentially expressed genes were identified using DESeq R package with FDR<0.001 and (|log2(Fold Change)|≥1
Enrichment analysis for GO using topGO R package and GO classification using WEGO 2.0 (wego.genomics.org.cn/)
Venn diagram of GO items performed using GOView (www.webgestalt.org/GOView/)
Genome_build: TGACv1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 13, 2018 |
| Last update date |
Aug 14, 2018 |
| Contact name |
Jun Wei |
| E-mail(s) |
weijun199052009@qq.com
|
| Phone |
+86 10 6283 6060
|
| Organization name |
Institute of Botany, CAS
|
| Department |
Key Laboratory of Plant Molecular Physiology, CAS
|
| Street address |
No.20 Nanxincun, Xiangshan
|
| City |
beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
| |
|
| Platform ID |
GPL23509 |
| Series (1) |
| GSE118474 |
Insights into transcriptional characteristics and homoeolog expression bias of embryo and endosperm in developing grain through mRNA-Seq and Iso-Seq |
|
| Relations |
| BioSample |
SAMN09813478 |
| SRA |
SRX4548919 |
