|
| Status |
Public on Jan 15, 2019 |
| Title |
pokc-rna |
| Sample type |
SRA |
| |
|
| Source name |
Pok control
|
| Organism |
Oryza sativa |
| Characteristics |
developmental stage: 24-day-old
cultivar: Pokkali (Pok)
tissue: seedlings
|
| Treatment protocol |
Approximately 24-day-old seedlings were subjected to salt stress with supplementation of 150 mM NaCl for 24 hours, while control samples were remained in Yoshida medium.
|
| Growth protocol |
Rice seedlings were grown in Yoshida medium in a controlled growth chamber (22–24°C) with a 16h/8h (day/night) photoperiod and 300 µmol m−2 s−1 light intensity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA and polysome RNA were isolated using Trizol® Reagent according to the manufacturer’s instructions (Invitrogen).
mRNA-Seq libraries were generated by following Illumina mRNA Sequencing Sample Preparation Guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
rice-RNA-seq-gene-fpkm.xlsx
|
| Data processing |
TopHat was used to align the reads to the genome of rice (MSU v6.1) with option “-G”.
Cufflinks was used to assemble the alignments from TopHat.
Cuffmerge was used to merged assembled transcripts from the individual libraries.
Cuffcompare was used to compare the combined transcripts to annotated transcripts on MSU Rice Genome Annotation Database (v6.1).
Cuffdiff was used to compare expression levels of the transcripts in the control and salt stress libraries.
Genome_build: rice (MSU v6.1)
Supplementary_files_format_and_content: FPKM values of genes
|
| |
|
| Submission date |
Sep 10, 2018 |
| Last update date |
Jan 15, 2019 |
| Contact name |
Yun Zheng |
| E-mail(s) |
zhengyun5488@gmail.com
|
| Organization name |
Yunnan Agricultural University
|
| Street address |
452 Fengyuan Road
|
| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650201 |
| Country |
China |
| |
|
| Platform ID |
GPL13160 |
| Series (2) |
| GSE119720 |
Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress [Total RNA] |
| GSE119722 |
Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress |
|
| Relations |
| BioSample |
SAMN10025564 |
| SRA |
SRX4665457 |
