|
| Status |
Public on May 23, 2016 |
| Title |
OE12-1 |
| Sample type |
SRA |
| |
|
| Source name |
CsFUS3 overexpression_12wk induction
|
| Organism |
Citrus unshiu |
| Characteristics |
strain/clone background: ‘Guoqing No.1’ Satsuma mandarin
genotype/variation: overexpressing CsFUS3 vector
treatment: 12 weeks of glycerol induction
time points during se: onset of the somatic embryo emergence
tissue: callus
|
| Treatment protocol |
Overexpression CsFUS3 vector and empty vector were transferred into ‘Guoqing No.1’ Satsuma mandarin (G1) callus, respectively.
|
| Growth protocol |
Callus of ‘Guoqing No.1’ Satsuma mandarin was preserved on MT medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol method
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the degestion products are purified by magnetic beads. After that, the mRNA is enriched by using the oligo(dT) magnetic beads (for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primed reverse transcription. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads . End reparation is then performed. After the previous step, adaptors are ligated to the ends of these fragments. Next, ligation products were selected by size and purified on TAE-agarose gel. Finally, the fragments are enriched by PCR amplification, then purified by magnetic beads and dissolved in the appropriate amount of Epstein-Barr solution.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
After removal of low quality reads and/or adaptor sequences, the clean reads were aligned to the genomic DNA sequence of sweet orange (Citrus sinensis)
The gene expression level was calculated by using RPKM method.
Differentially expressed genes were analysed based on the poisson distribution method.
Gene ontology enrichment analysis and KEGG enrichment analysis of differentially expressed genes
Genome_build: citrus sinensis whole genome（http://www.ncbi.nlm.nih.gov/assembly/GCF_000317415.1）
Supplementary_files_format_and_content: 8 files includes RPKM values
|
| |
|
| Submission date |
May 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Liu Zheng |
| Organization name |
Huazhong Agricultural University
|
| Street address |
No.1,Shizishan
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL20237 |
| Series (1) |
| GSE69193 |
Overexpression of a B3 Transcription Factor CsFUS3 Promotes Somatic Embryogenesis of citrus through the Abscisic Acid and Gibberellin |
|
| Relations |
| BioSample |
SAMN03733235 |
| SRA |
SRX1037501 |
