|
| Status |
Public on Jul 14, 2018 |
| Title |
ZDB475 As rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Barley
|
| Organism |
Hordeum vulgare |
| Characteristics |
cultivar: ZDB475
tissue: root
age: 25-30 days
phenotype: Arsenic sensitive
|
| Treatment protocol |
At three-leaf stage As and P treatments were performed by adding Na2HasO4 and Na2HPO4 into the basic nutrient solution, respectively to form 100 µM As and 50 µM P.
|
| Growth protocol |
Ten-days-old seedlings were transplanted into 1L plastic pots for hydroponic culture, with the basic nutrient solution. The BNS was renewed every 5 d. Initially the plants were supplied with half strength BNS for 7d thereafter full strength was supplied. At three-leaf stage As and P treatments were performed by adding Na2HasO4 and Na2HPO4 into the BNS, respectively to form 100 µM As and50 µM P.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA extraction, roots of 10 seedlings were collected and mixed together after 24 h of treatments. RNA extraction was done for 18 samples [2 genotypes × 3 treatments × 3 replicates] with TRIzol reagent following manufacturer instructions
RNA libraries were prepared for sequencing using standard BGI protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
wild type barley
|
| Data processing |
Sequencing read filtering was done using SOAPnuke software
Genome mapping was done using HISAT to align RNA-seq reads to the barley genome
Novel transcript, SNP and indel detection was done using StringTie and Cuffcompare
Gene ontology and pathway analysis of differentially expressed genes were done using Blast2GO
Transcription factor prediction was done by aligning the open reading frame to the transcription factor domain using hmmsearch.
Genome_build: http://webblast.ipk-gatersleben.de/barley_ibsc/downloads/
Supplementary_files_format_and_content: text files contain fpkm for genes per each sample
|
| |
|
| Submission date |
Jul 13, 2018 |
| Last update date |
Jul 16, 2018 |
| Contact name |
Gerald Zvobgo |
| E-mail(s) |
[email protected]
|
| Phone |
+8613185023089
|
| Organization name |
Zhejiang University
|
| Department |
Crop Science
|
| Lab |
Stress physiology
|
| Street address |
Yuhang
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310000 |
| Country |
China |
| |
|
| Platform ID |
GPL25328 |
| Series (1) |
| GSE117068 |
Transcriptomic comparison of two barley genotypes differing in arsenic tolerance exposed to arsenate and phosphate treatments |
|
| Relations |
| BioSample |
SAMN09654180 |
| SRA |
SRX4388436 |
