|
| Status |
Public on Apr 16, 2019 |
| Title |
fas_F&IM_R2 |
| Sample type |
SRA |
| |
|
| Source name |
floral and inflorescence meristems (F&IM)
|
| Organism |
Solanum pimpinellifolium |
| Characteristics |
tissue: floral and inflorescence meristems (F&IM)
genotype: fas mutant in LA1589 background
cultivar: LA1589
|
| Growth protocol |
Seeds were sown small pots and allowed to germinate under natural light supplemented with artificial light (16/8 hr light/dark cycle) in the greenhouse in Columbus, OH, USA, 2016. Approximately 300 first and second inflorescences with only 3-4 visible floral buds were collected from 5 to 7-week old plants that were sown over a six-week window.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
During the collection, all inflorescences were immediately immersed in ice-cold RNAlater (QIAGEN) solution at five times the volume of the sample in order to prevent RNA degradation. After sample collection, vacuum infiltration was applied until tissues sunk to the bottom of RNAlater solution. The tissues were then stored in RNAlater at -80℃. For the dissection, meristems and buds of different developmental stages were isolated by forceps under a dissection microscope and immediately put into a 1.5 ml eppendorf tube in 1 ml of fresh RNAlater that was kept on ice. The samples were stored at -80 ℃ prior to the RNA extraction. RNA extraction was conducted using Trizol® (Invitrogen Inc. USA) following manufacture’s recommendation.
3'Tag RNA-seq libraries of approximately 300 bp fragments were prepared following the 3’-Tagseq protocol of Meyer et al., (2011)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were filtered using fqtrim program with QC score< 20 as well as poly-A tail contaminations
Clean reads mapped to ITAG2.4 Released Tomato Genome through Rsubread 3.4
The significance of differentially expressed genes (DEGs) was determined by linear factorial modeling in DEseq2, of which likelihood ratio test was applied.
Genome_build: ITAG2.4 Released Tomato Genome
Supplementary_files_format_and_content: csv text files include read counts per gene for each sample
|
| |
|
| Submission date |
Apr 15, 2019 |
| Last update date |
Apr 16, 2019 |
| Contact name |
Esther van der Knaap |
| E-mail(s) |
EsthervanderKnaap@uga.edu
|
| Organization name |
University of Georgia
|
| Department |
Horticulture
|
| Street address |
111 Riverbend Rd
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL20002 |
| Series (1) |
| GSE129809 |
Expression analysis of tomato S. pimpinellifolium accession LA1589 wild type and the Nearly Isogenic Lines lc, fas and lc/fas NILs during floral development. |
|
| Relations |
| BioSample |
SAMN11417896 |
| SRA |
SRX5683714 |
