|
| Status |
Public on Mar 26, 2020 |
| Title |
32X-3 |
| Sample type |
SRA |
| |
|
| Source name |
fruit
|
| Organism |
Cucumis sativus |
| Characteristics |
tissue: fruit
genotype: inbred line 1461
|
| Growth protocol |
Near-isogenic lines 32X and GFC, northern China type cucumbers with short and light green fruits , were used in this study. The cucumber seeds were germinated in 28℃ in dark, and then the seedlings were transferred to a greenhouse under standard conditions in the experimental field of China Agricultural University in Beijing. Water management and pest control were performed according to standard protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fruits at anthesis of 32X and GFC cucumber plants were collected for RNA-seq analysis. Total RNAs were extracted using the RNA extraction kit (Huayueyang, Beijing, China). Three biological replicates were performed for each tissue sample. RNA-seq library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) according to the manufacturer’s instructions and four index codes were added to attribute sequences to different samples(Wang et al., 2009).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Cucumber genome sequence (http://cucumber.genomics.org.cn, v2i) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 RPM (readss per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values for 2 Samples .
|
| |
|
| Submission date |
Jan 30, 2019 |
| Last update date |
Mar 26, 2020 |
| Contact name |
Hailing Zi |
| E-mail(s) |
hlzi@sibs.ac.cn
|
| Organization name |
Shanghai center for plant stress biology
|
| Street address |
Chenhua road3888
|
| City |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL16310 |
| Series (1) |
| GSE125899 |
CsFUL1 and auxin participate in the CsCLV3-CsWUS mediated carpel number variation in cucumber (Cucumis sativus L.) |
|
| Relations |
| BioSample |
SAMN10847189 |
| SRA |
SRX5310973 |
