|
| Status |
Public on Apr 04, 2018 |
| Title |
Sequencing data from the shoot tips of one standard peach branch - standard tree #8 |
| Sample type |
SRA |
| |
|
| Source name |
Lateral shoot (branch) tips of trees
|
| Organism |
Prunus persica |
| Characteristics |
developmental stage: Mature tree
tissue: branch tip
growth habit: standard growth habit
|
| Treatment protocol |
No Treatments
|
| 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
50 bp RNAseq unpaired reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sequencing data from the shoot tips of one standard peach branch. This is a biological replicate. It is from a standard tree that we call #8
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) Hort Research. The standard trees used here are the same trees (and the same raw data) used for the RNAseq experiment described in Hollender et al (2018) PNAS and the pillar trees used for this study are from the same population as well.
|
| Data processing |
Barcodes were removed from Raw Reads and then the sequences were trimmed based on qualtiy and ambiguity using CLC Genomics workbench 10.1
The remaining reads were aligned against the Peach Genome Version 2 using CLC Genomics workbench 10.1
Differential expression analysis was performed using CLC Genomics workbench 10.1 Basic Variant Detection tool with the following modifications to the default parameters: Ploidy = 6, minimum coverage = 20, minimum count = 4, minimum frequency = 8.0.
Supplementary_files_format_and_content: TPM
|
| |
|
| Submission date |
Apr 03, 2018 |
| Last update date |
Apr 04, 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) |
| GSE112649 |
Alteration of TAC1 expression in Prunus species leads to pleiotropic shoot phenotypes |
|
| Relations |
| BioSample |
SAMN08851417 |
| SRA |
SRX3877960 |
