|
| Status |
Public on Mar 15, 2022 |
| Title |
SS-S-R1 |
| Sample type |
SRA |
| |
|
| Source name |
Root
|
| Organism |
Zea mays |
| Characteristics |
cultivar: SS
treatment: salinity
tissue: Root
developmental stage: three-leaf stage
|
| Treatment protocol |
At three leaf stage, seedlings were treated with water or 100 mM salinity solution.
|
| Growth protocol |
Maize plants were grown in normal conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Plant Mini Kit.
RNA libraries were prepared according to standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Clean reads were aligned to the maize reference genome (AGPv3) with Tophat2.
Aligned reads of single sample were assembled to generate transcripts with Cufflinks.
FPKM (expected fragments per kilobase of transcript per million fragments sequenced) values were evaluated by the Cuffdiff utility embedded in the Cufflinks package.
Genome_build: AGPv3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample. A fasta file with the novel transcript sequences is available on the series record.
|
| |
|
| Submission date |
Mar 18, 2019 |
| Last update date |
Mar 15, 2022 |
| Contact name |
Yijun Wang |
| E-mail(s) |
wyj@yzu.edu.cn
|
| Organization name |
Yangzhou University
|
| Street address |
Wenhui
|
| City |
Yangzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
225009 |
| Country |
China |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE128432 |
Transcriptomes of maize seedlings under water and salinity treatment |
|
| Relations |
| BioSample |
SAMN11158578 |
| SRA |
SRX5534389 |
