|
| Status |
Public on Mar 21, 2018 |
| Title |
weeping peach tree 4 |
| Sample type |
SRA |
| |
|
| Source name |
Lateral shoot (branch) tips of trees
|
| Organism |
Prunus persica |
| Characteristics |
developmental stage: Mature tree
tissue: branch tip
growth habit: weeping growth habit
|
| Growth protocol |
Trees were grown in a field at the USDA ARS Appalachian Fruit Research Station
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Omega SQ total RNA kit with the addition of 2% PVP to the lysis buffer
50 bp Illumina Truseq uppaired libraries were constructed at the gemoics resources core facility at Weill Cornell College of Medicine
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sequencing data from the shoot tips of one weeping peach branch. This is a biolical replicate. It is from a weeping tree that we call #4
These peach trees were from a segregating F2 population from a cross between parents used only for breeding purposes. The trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the paper Hollender et al (2018) PNAS.
|
| Data processing |
Barcodes were removed from Raw Reads and then the sequences were trimmed based on qualtiy and ambiguity using CLC Genomics workbench 9.5.3
The remaining reads were aligned against the Peach Genome Version 1 using CLC Genomics workbench 9.5.3
Differential expression analysis was perfuormed using CLC Genomics workbench 9.5.3 "Transcriptomics Analysis" function
Genome_build: https://www.rosaceae.org/organism/Prunus/persica
Supplementary_files_format_and_content: Excel file of CLC genomics workbench output of the differential expression analysis
|
| |
|
| Submission date |
Mar 20, 2018 |
| Last update date |
Mar 21, 2018 |
| Contact name |
Courtney Hollender |
| E-mail(s) |
chollend@msu.edu
|
| Phone |
517-353-0446
|
| Organization name |
Michigan State University
|
| Department |
Dept. of Horticulture
|
| Lab |
Hollender Lab
|
| Street address |
1066 Bogue St
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL15671 |
| Series (1) |
| GSE112080 |
RNAseq for peach weeping and standard lateral shoot (branch) tips |
|
| Relations |
| BioSample |
SAMN08742971 |
| SRA |
SRX3823845 |
