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Sample GSM7070999 Query DataSets for GSM7070999
Status Public on Feb 27, 2024
Title SSL rep2
Sample type SRA
 
Source name leaf
Organism Lactuca sativa
Characteristics tissue: leaf
location: Belle Glade, FL
tissue type: mature
genotype: 60184 (SSL)
Treatment protocol Three romaine lettuces (Lactuca sativa var. Longifolia) grown in Belle Glade, FL were selected for leaf tissue histological analysis, including the commercial cultivars ‘Manatee’, and ‘Okeechobee’ and an experimental breeding line named 60184. These accessions were selected from a larger set of romaine accessions based on genotypic variability in their shelf life
Growth protocol Lettuce plants were grown in 4-inch pots in a growth chamber maintained with a 16 h day light cycle at 22 ºC.
Extracted molecule total RNA
Extraction protocol Upon reaching maturity, RNA was extracted using the Nucleospin RNA Plant and Fungi kit (Machery-Nagel, Düren, Germany) with on-column DNase treatment, and initial quantification and quality was checked on a NanoDrop OneC spectrophotometer
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina Casava1.7 software used for basecalling.
The genome of Lactuca sativa (version: Lsativa_467_v5) from JGI (Joint Genome Institute, Berkeley, USA) was used as the reference genome for RNA-seq analysis. The cleaned reads of each sample were mapped individually to the reference sequences using the STAR package
The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2) (Anders et al., 2015), samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates, choose and count uniquely mapped reads for gene expression analysis
The counted reads of each gene were analyzed by a DESeq2-based R pipeline. Differentially expressed (DE) genes were analyzed in a pairwise comparison between genotypes 60814 and ‘Okeechobee’ samples. Transcripts per million (TPM) counts were averaged across biological replicates and genes were filtered for moderate expression (TPM ≥ 100) in at least one genotype.
Assembly: Arabidopsis thaliana , version: Lsativa_467_v5
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample
 
Submission date Feb 28, 2023
Last update date Feb 27, 2024
Contact name FAHONG YU
E-mail(s) fyu@ufl.edu
Phone 3522738064
Organization name UNIVERSITY OF FLORIDA
Department ICBR
Street address 2033 Morway RD
City GAINESVILLE
State/province FL
ZIP/Postal code 32608
Country USA
 
Platform ID GPL29850
Series (1)
GSE226302 Examining preharvest genetic and morphological factors contributing to lettuce (Lactuca sativa L.) shelf life
Relations
BioSample SAMN33483241
SRA SRX19523692

Supplementary file Size Download File type/resource
GSM7070999_S2_S2_count.txt.gz 168.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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