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| Status |
Public on Apr 08, 2020 |
| Title |
LNR2 |
| Sample type |
SRA |
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| Source name |
N Replete Root
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| Organism |
Spinacia oleracea |
| Characteristics |
cultivar: Banjo
tissue: Leaf
treatment: Low N
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| Growth protocol |
Samples collected from 6-week old plants were frozen in liquid nitrogen and stored at −80 °C until subsequent analyses. Three independent plants were used for metabolic analysis, total RNA extractions, physiological and biochemical analysis. The seeds of spinach variety ‘Banjo’ were grown in plastic containers containing Turface ® based growing medium under 200 μmol·m-·s-1light intensity(12 hours each light and dark period) at 23°C and 60-70% relative humidity. Two treatments, High N and low N, where N was added in the form of Ca(NO3)2 , were used to maintain the concentration of 200 ppm for High N and 50 ppm for low N. CaCl2 was compensated to keep the same concentration of calcium in both treatments. The concentrations of remaining macro- and micro-elements were kept constant using N-free Hoagland’s nutrient solution
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| Extracted molecule |
total RNA |
| Extraction protocol |
The flash-frozen plant samples in liquid nitrogen were ground to a fine powder using a paint shaker (Harbil, Wheeling, IL, USA) and 3-mm-diameter steel balls (Abbott Ball, West Hartford, CT, USA). Total RNA was extracted using an RNeasy® Plant Mini Kit (QIAGEN Sciences, Germantown, MD, USA) as per the manufacturer’s protocol and treated with DNase1 (QIAGEN Sciences, Germantown, MD, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
N Replete Root
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| Data processing |
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to Spinacia_oleracea whole genome using hisat2-2.1.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts
Differeantial expression analysis with DEseq2
Genome_build: Spinacia_oleracea V1.0
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion
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| Submission date |
Feb 26, 2020 |
| Last update date |
Apr 08, 2020 |
| Contact name |
Vijay Joshi |
| E-mail(s) |
[email protected]
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| Phone |
8302789151
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| Organization name |
Texas A&M AgriLife Research
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| Department |
Department of Horticultural Sciences
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| Street address |
1619 Garner Field Road
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| City |
Uvalde |
| State/province |
Texas |
| ZIP/Postal code |
78801 |
| Country |
USA |
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| Platform ID |
GPL28198 |
| Series (1) |
| GSE145943 |
RNA-Sequencing of nitrogen-stressed spinach tissue |
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| Relations |
| BioSample |
SAMN14210565 |
| SRA |
SRX7805396 |
| 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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