|
| Status |
Public on Jan 15, 2019 |
| Title |
ir29s-ps |
| Sample type |
SRA |
| |
|
| Source name |
polysomal fractions of IR29 salt stress
|
| Organism |
Oryza sativa |
| Characteristics |
developmental stage: 24-day-old
tissue: seedlings
cultivar: IR29
|
| 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 on 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 |
RNA was isolated from 10 µg each of the total RNA and polysomal RNA using MicroPoly(A) Purist ™ kit (Ambion).
Briefly, rice seedlings were ground into a fine powder with liquid nitrogen, then thoroughly mixed with polysome extraction buffer using a spatula and placed on ice for 10 min with occasional mixing by inverting tubes. The lysis was spun for 2 min at 14000 rpm (4 C) and the supernatant was passed through a QIA shredder (QIAGEN) column by centrifugation for 1 min at 14000 rpm (4 C). Approximately 600 microL of the sample was layered on top of the sucrose density gradients (20-60% sucrose, w/v) and centrifuged for 120 min at 40,000 rpm (275,000 g) in a Beckman OPTIMA LE-80 centrifuge. The optical density (OD) of the samples was measured by using a UA-5 detector and a Gradient Fractionator (model 640, ISCO) reading absorbance throughout the sucrose gradient at 254 nm. Fractions with more than two ribosomes were pooled and used for RNA isolation and RNA-Seq library preparation later.
mRNA-Seq libraries were generated by following Illumina mRNA Sequencing Sample Preparation Guide.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
rice-PS-seq-gene-fpkm.xlsx
|
| Data processing |
Library strategy: polysome-seq
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) |
| GSE119721 |
Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress [polysomal RNA] |
| GSE119722 |
Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress |
|
| Relations |
| BioSample |
SAMN10025479 |
| SRA |
SRX4665333 |
