|
| Status |
Public on Jan 19, 2017 |
| Title |
Phloem-3 |
| Sample type |
SRA |
| |
|
| Source name |
Phloem
|
| Organism |
Populus trichocarpa |
| Characteristics |
tissue: Phloem
age: 6 months
|
| Treatment protocol |
Shoot tip samples were obtained from the first to third internode, leaf samples were fully expanded young leaves, phloem was scraped from inner part of the bark, and xylem samples were stem secondary developing xylem collected by scraping from surface of debarked stems as we did previously (Shi et al., 2010). Root samples were primary roots collected from young seedlings rooted in water. Cell samples containing fiber cells, vessel cells, or a mixture of three different cell types (fiber, vessel, and ray) were collected from 6-month-old greenhouse grown P. trichocarpa by using a LMD7000 (Leica).
|
| 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 greenhouse for 6 months (16 h light/8 h dark cycle with supplemental light of ~300 µE m-2 s-1) before tissue was harvested for characterization.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen), and RNAs of LCM samples were amplified using Arcrurus RiboAmp HS PLUS kit (Life Technology).
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 |
| |
|
| Description |
Processed data file: Tissue_LCM_rawcount.txt
|
| 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 (JGI Phytozome V11, https://phytozome.jgi.doe.gov/pz/portal.html) using the program "TOPHAT".
Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: Tissue_LCM_rawcount.txt: Tab-delimited text file with Phytozome Populus trichocarpa gene model names (version 3) and the read counts.
|
| |
|
| Submission date |
May 03, 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 (1) |
| GSE81077 |
RNA-seq of major tissues and xylem cell types of Populus trichocarpa |
|
| Relations |
| BioSample |
SAMN04939129 |
| SRA |
SRX1740293 |
