|
Status |
Public on Jul 17, 2021 |
Title |
HC-FTAZ:PCBM-3 |
Sample type |
SRA |
|
|
Source name |
leaf
|
Organism |
Lactuca sativa |
Characteristics |
intensity experiment: Height Controlled opv filter: FTAZ:PCBM 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 |
Jun 14, 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 |
GPL30397 |
Series (1) |
GSE180179 |
Transcriptome of red oak leaf lettuce grown under OSC filters |
|
Relations |
BioSample |
SAMN20248944 |
SRA |
SRX11464902 |