|
| Status |
Public on Jan 01, 2018 |
| Title |
84 control rep1 |
| Sample type |
SRA |
| |
|
| Source name |
shoot
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: shoot
genotype: 84
age: 8 days old
|
| Treatment protocol |
Salinity stress (6:1 molar ratio, NaCl:CaCl2) was increased to 6 dS·m-1 gradually in two 3 dS·m-1 intervals over a period of 24h. After 24h of 6 dS·m-1, aerial parts of the seedlings were excised from the roots and frozen immediately in liquid nitrogen.
|
| Growth protocol |
Briefly, plants were grown in a controlled environment growth chamber. Seedlings were transplanted into the pots filled with Turface (Profile Products, LLC) and were grown in tap water for two days after transplanting. For the remainder of the experiment the plants were supplemented with half strength Yoshida solution (pH 5.8). Temperatures were maintained at 28 °C and 25 °C in day and night respectively, relative humidity was maintained at 60% in both day and night. Lighting was maintained at 800 μmoles·m−2·s−1 using high pressure sodium lights.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The samples were ground with Tissuelyser II (Invitrogen) and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
96 libraries were prepared using TruSeq RNA v2 library preparation reagents. Eighteen samples were sequenced per lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RDP1: NSFTV_84
|
| Data processing |
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to rice genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each gene with htseq-count
Genome_build: Oryza sativa japonica reference genome v 6
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts
|
| |
|
| Submission date |
May 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chi Zhang |
| E-mail(s) |
czhang5@unl.edu
|
| Organization name |
University of Nebraska - Lincoln
|
| Street address |
1901 Vine Street
|
| City |
Lincoln |
| State/province |
NE |
| ZIP/Postal code |
68588 |
| Country |
USA |
| |
|
| Platform ID |
GPL19290 |
| Series (1) |
| GSE98455 |
Variation in transcriptional responses to salt stress in rice |
|
| Relations |
| BioSample |
SAMN06860808 |
| SRA |
SRX2776434 |
