|
| Status |
Public on Jul 27, 2021 |
| Title |
CHI9, rep4a |
| Sample type |
SRA |
| |
|
| Source name |
glandular cells of type VI trichome
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: leaf type VI glandular trichomes
sampling time: #4
genotype/variation: complemented line #9
|
| Treatment protocol |
Glandular cells of type VI trichome was collected as described in Schilmiller et al. (2010) Plant Physiology 153: 1212-1223.
|
| Growth protocol |
Plants grew on the potted soil in the growth chamber under 250 μE and 28 ºC for 5 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy kit (Qiagen) according to the manufacturer's instructions.
Sequencing libraries were prepared from total RNA with the TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Lane 1
|
| Data processing |
Sequence reads were trimmed using the Trimmomatic software (Bolger et al., 2014) to eliminate adaptor sequences and low quality reads.
The remaining reads were mapped to the Solanum lycopersicum L. reference genome sequence (ITAG 2.5 genome) using Tophat2 software (Kim et al., 2003).
The mapped reads were then aligned using SAMtools (Li et al., 2009) and counted by HTSeq (Anders et al., 2015).
Genome_build: ITAG2.4_gene_models.gff3 (ITAG 2.4 is gene structure information, ITAG 2.5 is genome assembly)
Supplementary_files_format_and_content: *_20_sorted_n_count2.count.txt: HTSeq count data; tab-delimited text files include cpm values for each sample.
|
| |
|
| Submission date |
Aug 02, 2018 |
| Last update date |
Jul 27, 2021 |
| Contact name |
koichi Sugimoto |
| E-mail(s) |
sugimok@msu.edu
|
| Organization name |
Michigan State University
|
| Street address |
612 Wilson Rd
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE118065 |
Gene expression in the tomato trichome collected from af mutant and its complemented lines |
|
| Relations |
| BioSample |
SAMN09761969 |
| SRA |
SRX4503554 |
