|
| Status |
Public on Jan 17, 2014 |
| Title |
miR397-line17 |
| Sample type |
SRA |
| |
|
| Source name |
developing xylem
|
| Organism |
Populus trichocarpa |
| Characteristics |
genetic background: Nisqually-1
tissue: developing xylem
genotype: over expression miR397a
|
| Treatment protocol |
transgenic overexpression PtrMIR397a with CaMV 35s promoter
|
| Growth protocol |
P. trichocarpa plants were grown in pots containing half Miracle- Gro Soil (Scotts Miracle-Gro, Maysville, OH) and half Metro-Mix 200 (Sun Gro, Bellevue, WA) in a greenhouse at 17–26 °C, 16 h light/8 h dark cycle (with supplemental light of ~300 μE/m2/s). Miracle-Gro Plant Food (Scotts Miracle-Gro) was applied once a week
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolted using the CTAB method (Chang et al. 1993. Plant Mol Biol Rep 11: 113-116).
TruSeq RNA Sample Prep v2 LS protocol (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
mapped to Populus trichocarpa v3 using TopHat v2.0.3 and bowtie b0.12.7 with command tophat -p 7 -G /genomes/ptrichocarpa/sequences/Ptrichocarpa_210_gene_exons.gff3 /genomes/ptrichocarpa/index/Ptrichocarpa_210.fa *.fq
convert mapped file to depth file by coverageBed v2.14.2 with parameter coverageBed -abam */accepted_hits.bam -b genomes/ptrichocarpa/sequences/Ptrichocarpa_210_gene_exons.gff3 > *.rawcount
compile rawcount file from all libraries into tab-delimited text file using perl script
Genome_build: Populus trichocarpa version 3.0 (www.phytozyme.com)
Supplementary_files_format_and_content: tab-delimited text files raw count values of transcript for each sample
|
| |
|
| Submission date |
Jan 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sermsawat Tunlaya-anukit |
| E-mail(s) |
stunlay@ncsu.edu
|
| Phone |
+1 919-802-8712
|
| Organization name |
North Carolina State University
|
| Department |
Department of Forestry and Environmental Resources
|
| Lab |
Forest Biotechnology Group
|
| Street address |
840 Main campus drive room2500
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27 |
| Country |
USA |
| |
|
| Platform ID |
GPL17415 |
| Series (1) |
| GSE54153 |
Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa |
|
| Relations |
| BioSample |
SAMN02585420 |
| SRA |
SRX435200 |
