|
| Status |
Public on Feb 01, 2025 |
| Title |
young inflorescence of progeny with fw2.3-D genotype replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
young inflorescence
|
| Organism |
Solanum lycopersicum var. cerasiforme |
| Characteristics |
tissue: young inflorescence
genotype: fw2.3-D
|
| Treatment protocol |
Young inflorescence tissues with the largest floral buds smaller than 2mm long were removed from plants by a forcep and immediately frozen in liquid nitrogen
|
| Growth protocol |
tomato plants were cultivated in greenhouse condition without pruning. Plants with contrasting genotypes were arranged randomly and received same lighting and watering condition prior to tissue collection.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from the ground tissues using Trizol reagent (Life technologies) according to the manufacture’s specifications. The quality and quantity of the RNA were examined by Agilent Bioanalyzer 2100 system (Agilent Technologies) at the Georgia Genomics and Bioinformatics Core at University of Georgia, Athens. Equal quantity of RNA from two plants of the same fw2.3 genotype was pooled to form six pools, three of each genotype.
Non-strand-specific RNA library construction was performed by Novogene library construction service
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Library name: A3_CRRA200011723-1a_H57KFDSXY_L1
|
| Data processing |
The sequencing reads were trimmed by the Cutadapt tool and aligned to SL4.0 reference genome using STAR RNA-seq aligner
the read count was carried out by R package Rsubread. Reads normalization and differential expression analysis was performed using R package edgeR; genes with log2 FC > 1 or < − 1 and p-value < 0.05 were considered as differentially expressed.
Assembly: SL4.0
Supplementary files format and content: individual Comma-separated values file contains raw read count for each sample
Supplementary files format and content: Comma-separated values file contains normalized RPKM of all samples
|
| |
|
| Submission date |
Jan 28, 2025 |
| Last update date |
Feb 01, 2025 |
| Contact name |
Esther van der Knaap |
| E-mail(s) |
esthervanderknaap@uga.edu
|
| Organization name |
UNIVERSITY OF GEORGIA
|
| Street address |
111 Riverbend Rd
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30605 |
| Country |
USA |
| |
|
| Platform ID |
GPL35336 |
| Series (1) |
| GSE288202 |
RNA-seq data from tomato young inflorescence segregating for fruit weight QTL fw2.3 |
|
| Relations |
| BioSample |
SAMN46389773 |
| SRA |
SRX27450177 |
