|
| Status |
Public on Jul 13, 2012 |
| Title |
12dpp |
| Sample type |
SRA |
| |
|
| Source name |
Fruit during early development
|
| Organism |
Cucumis sativus var. sativus |
| Characteristics |
cultivar: Vlaspik
tissue: pericarp, placenta
developmental stage: 12 days post polination
|
| Growth protocol |
Sets of 80 cucumber plants per experiment were grown in the greenhouse in 3.78 L plastic pots filled with BACCTO (Michigan Peat Co., Houston, TX) media and fertilized once per week. Temperature was kept between 21 to 25 °C, supplemental lights were used to provide an 18 h light period. Pest control was performed according to standard management practices. All flowers for each experiment were hand pollinated on a single date (1-2 flowers per plant). The experiment was repeated three times.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA and cDNA sample preparation were based on the procedures of Schilmiller et al. (PNAS (2009) 106:10865-10870) and Ando and Grumet (J Am Soc Hort Sci (2010) 135:176-182).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS |
| |
|
| Description |
SRP013979
SRX157289
|
| Data processing |
Basecalls were performed with Roche/454 gsRunProcessor
Reads were screened and filtered using DFCI Gene Indices tools SeqClean pipeline (http://compbio.dfci.harvard.edu/tgi/software/)
Cleaned reads were assembled in to contigs using TGI Clustering Tools (TGICL, http://compbio.dfci.harvard.edu/tgi/software/) followed by CAP3
Number of reads from each sample contributing to each contig were counted.
Genome_build: n/a
Supplementary_files_format_and_content: tab delimited text with column headers: column 1 gb accession from transcriptome shotgun assembly TSA submission; column 2 internal contig name; column 3 total reads from all samples contributing to contig; column 4 length of contig in nt; columns 5-9 normalized representation of each sample for contig, TPT==Transcripts per Thousand.
|
| |
|
| Submission date |
Jul 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin M Carr |
| E-mail(s) |
carrk@msu.edu
|
| Organization name |
Michigan State University
|
| Department |
Research Technology Support Facility
|
| Street address |
Plant Biology Lab, 612 Wilson Rd., Rm. S-20 A
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL15801 |
| Series (1) |
| GSE39310 |
Cucumber transcriptome tells story of early fruit development from fruit set through exponential growth |
|
| Relations |
| BioSample |
SAMN02197480 |
| SRA |
SRX157289 |
