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| Status |
Public on Feb 25, 2021 |
| Title |
XC3 |
| Sample type |
SRA |
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| Source name |
10 uM H3BO3 for 15 weeks
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| Organism |
Citrus sinensis |
| Characteristics |
tissue: Root tips
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| Treatment protocol |
Plants were irrigated with Hogland’s nutrient solution containing 10 (control) or 400 (B-toxic) μM H3BO3 every other day for 15 weeks
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| Growth protocol |
11-week-old Citrus sinensis and C. grandis seedlings were sand cultured in ceramic pots, grown in a greenhouse under natural photoperiod and environmental temperature.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Root total RNA was extracted with the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Approximately 1 μg of mixed total RNA from five replicates was used to prepare a small RNA (sRNA) library with the TruSeq Small RNA Sample Prep Kit (Illumina, USA) according to the manufacturer’s protocol. The sRNA libraries were gel-purifid in 6% PAGE gels, and their concentration was then diluted to 2 ng/μl. The insert size of the sRNA libraries was tested with an Agilent 2100 bioanalyser. Aftr accurate quantifiation via qRT-PCR, single-end sequencing was performed on an Illumina HiSeq 2500.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Control treatments
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| Data processing |
The raw reads obtained from high-throughput sequencing were subjected to the Illumina pipeline filter for removement of adapter dimers, junk and low-complexity sequences, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Clean reads were subjected to BLAST searches against miRBase 21 (http://www.mirbase.org/) to identify known miRNAs.
The remaining non-annotated sequences of 18-30 nucleotides (nt) in length were mapped to the Citrus clementina genome (JGI version 1.0, http://www.phytozome.org/clementine.php) with the MTide program (http://bis.zju.edu.cn/MTide) to identify novel miRNAs.
Both the fold-change and P-value of each miRNA identified in each library were calculated using DESeq software, and the P-value was then adjusted to the false discovery rate (FDR) according to the Benjamini Hochberg Method. A 1.5-fold cut-off was set for determination of up- and down-regulated miRNAs, in addition to a FDR of less than 1.
Target genes of miRNAs obtained were predicted using TargetFinder.
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| Submission date |
Feb 26, 2018 |
| Last update date |
Feb 25, 2021 |
| Contact name |
Jing-Hao Huang |
| E-mail(s) |
jhuang1982@126.com
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| Phone |
+8613675012724
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| Organization name |
Fujian Academy of Agricultural Sciences
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| Department |
Pomological Institute
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| Street address |
Wusi Road
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| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350013 |
| Country |
China |
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| Platform ID |
GPL21082 |
| Series (1) |
| GSE111128 |
Illumina miRNA sequencing revealed Citrus adaptation to long-term B-toxicity through modulation of lateral root development by miR319 |
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| Relations |
| BioSample |
SAMN08607501 |
| SRA |
SRX3742484 |
| 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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