|
| Status |
Public on Jul 26, 2022 |
| Title |
Citrus unshiu, control [CK RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
shoots; mature stems
|
| Organism |
Citrus unshiu |
| Characteristics |
treatment: normal water
tissue: shoots; mature stems
genotype: WT
time: Day 75
|
| Treatment protocol |
At the beginning of the water deficit treatment, trees were fully watered, and soil moisture was measured at 9:00 am every day using the soil moisture meter (Zhejiang TOP Cloud-Agri Technology Co., Ltd, Zhejiang, China), followed by the evaporation of soil water naturally until reaching the set level (around 15%). The LD treatment lasted 75 days.
|
| Growth protocol |
All the plants were grown in the rain-proof plastic tunnel of Zhejiang citrus institute (Zhejiang, China), and 20 healthy trees were selected for water deficit treatment and control, respectively. 1–1.5 m growing in an 80-cm plastic root-limiter containing a potting mix of goat manure and clay (7:3) . The trees in the greenhouse were exposed to natural variations in photoperiod throughout the experiment for 5 months (from October to flower bud appearance) from 2020 to 2021
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026. 2 µg of total RNAs wasere used for to strandedstandardize the RNA sequencing library.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) according to following the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw sequencing data was initially first filtered by Trimmomatic (version 0.36), low-quality reads were discarded, and the reads contaminated with adaptor sequences were trimmed
Clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the the same cluster.
Reads in the the same cluster were compared to each other by pairwise alignment, followed by extraction into a new sub-cluster of and then reads with sequence identity over 95% were extracted to a new sub-cluster.
Al the sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters.
Assembly: Citrus sinensis v1.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
May 13, 2022 |
| Last update date |
Jul 26, 2022 |
| Contact name |
Bei Huang |
| Organization name |
Zhejiang citrus research institute
|
| Street address |
Daqiao street No.157
|
| City |
Taizhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
318026 |
| Country |
China |
| |
|
| Platform ID |
GPL32252 |
| Series (2) |
| GSE202925 |
Transcriptome analysis of flowering branches building of Citrus plants induced by light drought (LD) condition [RNA-seq] |
| GSE202927 |
Transcriptome and Methylome analysis of flowering branches building of Citrus plants induced by light drought (LD) condition |
|
| Relations |
| BioSample |
SAMN28230219 |
| SRA |
SRX15249846 |
