|
| Status |
Public on Mar 07, 2016 |
| Title |
NSF1_i7-2-2 |
| Sample type |
SRA |
| |
|
| Source name |
Stem differentiating xylem
|
| Organism |
Populus trichocarpa |
| Characteristics |
gene perturbation type: knockdown of PAL2,PAL4,PAL5
batch of trees: NSF1
tissue: Stem differentiating xylem
|
| Treatment protocol |
Agrobacterium mediated transformation of binary vector to knockdown or overexpression target genes driven by xylem specific promoter of 4-coumarate:CoA ligase gene[EU603323]
|
| Growth protocol |
P. trichocarpa Wild type and transgenic 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 6 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 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 Genome Analyzer IIx |
| |
|
| Data processing |
Six to twelve libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for Illumina GAIIx or HiSeq 2000 sequencing
68 to 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: Populus trichocarpa gene model name (version 3)
Supplementary_files_format_and_content: xlsx file with phytozome Populus trichocarpa gene model name (version 3) and the read counts
|
| |
|
| Submission date |
Mar 07, 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 |
GPL17579 |
| Series (1) |
| GSE78953 |
RNAseq of xylem tissue of transgenic and wildtype Populus trichocarpa (NSF Plant Genome Research Program Project 0922391) |
|
| Relations |
| BioSample |
SAMN04536079 |
| SRA |
SRX1616493 |
