|
| Status |
Public on Feb 01, 2018 |
| Title |
JG9-1 |
| Sample type |
SRA |
| |
|
| Source name |
Citrus
|
| Organism |
Citrus japonica |
| Characteristics |
tissue: Fruit
development stage: The five developmental stages of Clementine mandarin fruit were collected at 15, 30, 45, 80 and 120 days after flowering (DAF)
cultivar: Kumquat
|
| Treatment protocol |
No treatment
|
| Growth protocol |
The materials from Clementine mandarin and Kumquat were collected in the experiment fields of the National Citrus Breeding Center at Huazhong Agricultural University (30°28′ N, 114°21′ E, 30).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Life Technologies), and then treated with RNase-free DNase I (Life Technologies), according to the manufacturer's instructions.
Total RNA was sent to Beijing Genomics Institute (Shenzhen, China) where the libraries were produced and sequenced using Illumina's Genome Analyzer (Solexa).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequence reads were filtered for quality using the FASTX-Toolkit (Blankenberg et al. 2010) with default parameters by removing low-quality reads, and adaptor sequences. All clean reads were mapped to the citrus reference genome (Wu et al. 2014) using HISAT software (Kim et al. 2015) with default settings. Next, transcripts were assembled individually for each by StringTie (Pertea et al. 2015). Assembled transcripts were combined using Cuffmerge and then compared to annotation using Cuffcompare (Trapnell et al. 2012). Differential expression analysis was performs using the DESeq2 package (Love et al. 2014). A padj < 0.05 and 4-fold difference were used as a cutoff to identify differential expression genes (DEGs).
Genome_build: GCF_000493195.1
Supplementary_files_format_and_content:FPKM represent the expression of genes.
|
| |
|
| Submission date |
Dec 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
jin zhi zhang |
| E-mail(s) |
[email protected]
|
| Phone |
86-27-87281899
|
| Organization name |
Huazhong Agricultural University
|
| Department |
College of Horticulture and Forestry Science
|
| Street address |
College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
|
| City |
WuHan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL24351 |
| Series (1) |
| GSE107812 |
Genome-wide genetic variation identification and fruit-associated trait comparisons between kumquat (Fortunella japonica) and Clementine mandarin |
|
| Relations |
| BioSample |
SAMN08143815 |
| SRA |
SRX3453462 |
