|
| Status |
Public on Jun 03, 2014 |
| Title |
Florentine_Low_KPY_3 |
| Sample type |
SRA |
| |
|
| Source name |
Florentine_Low_KPY
|
| Organism |
Eucalyptus nitens |
| Characteristics |
strain: Low_KPY
tissue: xylem
age: 20 years
|
| Treatment protocol |
Trees from KPY extremes were sampled
|
| Growth protocol |
Trees are growing in natural environment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cambial scraps from trees were flash frozen on dry ice, and RNA was harvested using modified CTAB method. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 6
|
| Data processing |
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed low-quality sequence, then mapped to Eucalyputs grandis reference genome using Tophat
Read counts of each gene were used for differential gene expression analyis with edgeR package. Raw red counts were used in edgeR packge. BAM files from TopHat package were analyzed with BEDTools packaged to obtain read counts mapping to different transcripts represented in the GTF annotation file. These read counts were used in statistical tests of differential expression between control and stress treatments.
Genome_build: Egrandis_v1.0 [http://www.phytozome.net/eucalyptus.php]
Supplementary_files_format_and_content: tab-delimited text files include readcounts for each gene and each sample
|
| |
|
| Submission date |
Apr 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Saravanan Thavamanikumar |
| E-mail(s) |
saro.t@csiro.au
|
| Phone |
+61262464742
|
| Organization name |
CSIRO
|
| Street address |
Clunies Ross Street
|
| City |
Acton |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18542 |
| Series (1) |
| GSE56592 |
RNA-Seq using two populations reveals genes and alleles controlling wood traits and growth in Eucalyptus nitens |
|
| Relations |
| BioSample |
SAMN02721389 |
| SRA |
SRX513000 |
