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| Status |
Public on Feb 27, 2024 |
| Title |
SSL rep3 |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Lactuca sativa |
| Characteristics |
tissue: leaf
location: Belle Glade, FL
tissue type: mature
genotype: 60184 (SSL)
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| 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
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| 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.
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Feb 28, 2023 |
| Last update date |
Feb 27, 2024 |
| Contact name |
FAHONG YU |
| E-mail(s) |
fyu@ufl.edu
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| Phone |
3522738064
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| Organization name |
UNIVERSITY OF FLORIDA
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| Department |
ICBR
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| Street address |
2033 Morway RD
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| City |
GAINESVILLE |
| State/province |
FL |
| ZIP/Postal code |
32608 |
| Country |
USA |
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| Platform ID |
GPL29850 |
| Series (1) |
| GSE226302 |
Examining preharvest genetic and morphological factors contributing to lettuce (Lactuca sativa L.) shelf life |
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| Relations |
| BioSample |
SAMN33483240 |
| SRA |
SRX19523693 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7071000_S3_S3_count.txt.gz |
169.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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