|
| Status |
Public on Apr 21, 2022 |
| Title |
Control, PC4 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: leaf
genotype: wildtype
cultivar: Moneymaker
intensity experiment: PPFD Controlled (PC)
osc filter: Control
treatment: C_PC
|
| Treatment protocol |
OSC filter vs spectrally neutral control
|
| Growth protocol |
growth chamber under ceramic metal halide + incandescent bulbs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PureLink RNA Mini on-column kit with TRIzol with on-column DNAse treatment
mRNA library was prepped by BGI Genomics Co., Ltd. with polyA selection by an oligo dT library
All 31 samples were multiplexed, pooled and loaded together onto a DNBSEQ Technology Platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
DNBSEQ Technology Platform
|
| Data processing |
QC metrics were obtained using FastQC and high-quality (Q>30) read pairs were mapped to RefSeq GCF_000188115.4 using HISAT2 with default parameter settings
Aligned reads were assigned genomic features according to RefSeq GCF_000188115.4 annotations using featureCounts and read abundances quantified at the gene-level with default parameter settings
Raw counts were filtered for zero and low counts (<2) and library normalization was performed using DESeq2 size factor estimates
Assembly: RefSeq GCF_000188115.4
Supplementary files format and content: Text files with counts for each sample by gene
|
| |
|
| Submission date |
Apr 18, 2022 |
| Last update date |
Apr 23, 2022 |
| Contact name |
Heike Sederoff |
| E-mail(s) |
hwsedero@ncsu.edu
|
| Organization name |
North Carolina State University
|
| Department |
Plant & Microbial Biology
|
| Lab |
Sederoff Lab
|
| Street address |
851 Main Campus Dr
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695-7612 |
| Country |
USA |
| |
|
| Platform ID |
GPL28981 |
| Series (1) |
| GSE200978 |
Transcriptome of tomato leaf tissue grown under OSC filters |
|
| Relations |
| BioSample |
SAMN27621199 |
| SRA |
SRX14891679 |
