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| Status |
Public on Mar 01, 2024 |
| Title |
TTDV_Indiana(TX)_2019_S41 |
| Sample type |
SRA |
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| Source name |
Fruit
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| Organism |
Cucumis melo |
| Characteristics |
tissue: Fruit
cultivar: TTDV
location: Indiana(TX)
year: 2019
genotype: WT
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| Growth protocol |
The plants were grown during the spring growing season (March–June 2019) in fields located at the Texas A&M AgriLife Research Center – Texas A&M University System in Weslaco, Texas (latitude 26° 9' N, longitude 97° 57' W; elevation 21 m). In addition, F39 and TTDV plants were grown in TX (Uvaldi, 2018 and 2019), GA, NC, CA, IN, and AZ in 2019. Fruits were harvested at maturity (approximately 45 days after flowering).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 0.25 g of the powdered, frozen tissues were mixed with 1 ml of Trizol reagent (ThermoFisher) and incubate for 5 minutes. The solution was mixed with 0.5 ml of chloroform and centrifuged at 12,000g for 10 minutes after incubation for 5 minutes. The aqueous phase was mixed with 350 µl of ethanol and loaded to an EconoSpin column (Epoch Life Science), and centrifuged at 8,000 g for 40 seconds. The column was washed twice with 450 µl of 3M sodium acetate and with 320 µl of 70% ethanol. RNA was eluted with 30 µl of RNase-free water. Subsequently, RNA samples were treated with DNase and cleaned up with phenol-chloroform extraction and ethanol precipitation.
cDNA libraries were synthesized using Universal Plus mRNA-seq with NuQuant Kit (NuGen) according to the manufacturer's protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Location_normalized_VST.csv
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| Data processing |
The raw RNA-seq expression data were pre-processed by filtering out the transcripts with count per million (CPM) below 1 (low expressed transcripts).
Then the data were normalized following the DESeq function implemented in the DESeq2 R package after adjusting for the known biological melon sample covariates of cultivar location, fruit type, and binary Tobacco ringspot virus (TRSV) contamination status.
The binary TRSV contamination status of samples was determined by checking for any unmapped TRSV sequences in melon fruit sample sequences.
Following the instructions from DESeq2 data processing pipeline, we then performed variance stabilizing transformation (VST) on the RNA-seq data by the vst function implemented in the DESeq2 package.
Assembly: CM3.6.1_pseudomol http://cucurbitgenomics.org/ftp/genome/melon/DHL92/v3.6.1/
Supplementary files format and content: Fruit_normalized_VST.csv (The geneIDs are available on Melon DB https://melonet-db.dna.affrc.go.jp/ap/top)
Supplementary files format and content: Location_normalized_VST.csv (The geneIDs are available on Melon DB https://melonet-db.dna.affrc.go.jp/ap/top)
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| Submission date |
Mar 23, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Hisashi Koiwa |
| E-mail(s) |
koiwa@tamu.edu
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| Phone |
979-845-5282
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| Organization name |
Texas A&M University
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| Department |
Department of Horticultural Sciences
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| Street address |
495 Horticulture Rd.
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| City |
College station |
| State/province |
Texas |
| ZIP/Postal code |
77843 |
| Country |
USA |
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| Platform ID |
GPL30269 |
| Series (1) |
| GSE228039 |
RNA-seq data of melon fruits produced in different locations |
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| Relations |
| BioSample |
SAMN33871283 |
| SRA |
SRX19757119 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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