|
| Status |
Public on Jul 17, 2021 |
| Title |
PC-FTAZ:IT-M-4 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Lactuca sativa |
| Characteristics |
intensity experiment: PAR Controlled
opv filter: FTAZ:IT-M
tissue: leaf
|
| Treatment protocol |
Ceramic metal halide and incandescent lighting filtered through either 1 OPV filter or clear glass control, adjusted for light intensity (PAR controlled) or not adjusted for light intensity (Height Controlled)
|
| Growth protocol |
16 plants were grown per box, 2 plants per pot until "transplant" harvest at 3 weeks, 8 plants were grown to final harvest at 5 weeks, water and fertilizer were provided with automated irrigation system, pots were rotated every 2 days to prevent positional effects; leaf tissue was collected from 4 plants per treatment
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
TRIzol + PureLink RNA Mini kit, on-column DNAse and DNAse I treatment
Library was prepared by BGI Genomics Co., Ltd., poly A selection with oligo dT library, all 32 samples were pooled and loaded into all 3 lanes
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G50 |
| |
|
| Data processing |
QC metrics were obtained using FastQC and high-quality (Q>30) read pairs were mapped to Lsat_Salinas_v7 genome assembly using HISAT2 with default parameter settings
Aligned reads were assigned genomic features according to Lsat_Salinas_v7 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
Genome_build: GCA_002870075.2_Lsat_Salinas_v7
Supplementary_files_format_and_content: Text files with counts for each of the 32 samples by gene
|
| |
|
| Submission date |
Jul 15, 2021 |
| Last update date |
Nov 15, 2021 |
| 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 |
GPL30397 |
| Series (1) |
| GSE180179 |
Transcriptome of red oak leaf lettuce grown under OSC filters |
|
| Relations |
| BioSample |
SAMN20249148 |
| SRA |
SRX11464875 |
