|
| Status |
Public on Dec 27, 2018 |
| Title |
Day5-4 |
| Sample type |
SRA |
| |
|
| Source name |
Stem differentiating xylem
|
| Organism |
Populus trichocarpa |
| Characteristics |
days after drought treatment: 5 day
|
| Treatment protocol |
Control plants (day 0) are with fully irrigation, the soil water content is 74% and the xylem water content is 80.6%. After 5 days without watering, the drought treated plant (day 5) are under a mild drought state, and the soil and xylem water content in dropped to 33% and 75.3%, respectively. After 7 days without watering, the drought treated plant (day 7) is in a severe drought state where the soil and xylem water content continued decreasing to 29% and 74.3%, respectively.
|
| Growth protocol |
P. trichocarpa trees were grown in ½ Mircle-Gro Soil (Scotts Miracle-Gro products, Maysville, OH, USA) and ½ Metro-Mix 200 (Sun Gro, Bellevue, WA, USA) in the green house for 3 monthes (16 h light/8 h dark cycle with supplemental light of ~ 300 µE m-2 s-1) before tissue harvested for characterzation. Due to limited greenhouse space, different batch of transgenic trees with respective wild type were planted in soil and harvest at different time, there are total six batch trees were labeled with NSF1 to NSF6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Stem defferentiating xylem were scraped from the surface of the debark stem 5cm above soil using a single-edge razor into liquid nitrogen immediately. collected tissues were ground into powder and stored in liquid nitrogen. Total RNA of SDX sample were extracted by uing Qiagen RNeasy Mini Kit (Invitrogen/Life Technologies, Grand Island, NY) with DNase I treatment option as suggested by kit manunal.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Twelve libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for HiSeq 2000 sequencing
100 bp average read lengths were obtained after removing the library sequence index sequences from each read, reads were mapped to the reference P. trichocarpa genome release V3.0 (Phytozome V10.0, http://www.phytozome.com) using the program “TOPHAT”.
Genome_build: P. trichocarpa
Supplementary_files_format_and_content: xlsx file with phytozome Populus trichocarpa gene model name (version 3) and the read counts
|
| |
|
| Submission date |
Mar 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Vincent L Chiang |
| E-mail(s) |
vchiang@ncsu.edu
|
| Organization name |
North Carolina State University
|
| Department |
Forestry and Environmental Resources
|
| Lab |
Forest Biotechnology Group
|
| Street address |
840 Main Campus Drive
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
|
| Platform ID |
GPL17415 |
| Series (2) |
| GSE79401 |
RNAseq of drought treated Populus trichocarpa |
| GSE81048 |
Integrative analysis of genome-wide histone H3 lysine 9 acetylation and gene expression in *Populus trichocarpa* under drought stress reveals that AREB1 transcription factors recruit the GCN5-ADA2b complexes to activate drought-inducible gene expression |
|
| Relations |
| BioSample |
SAMN04569090 |
| SRA |
SRX1644029 |
