|
| Status |
Public on May 23, 2020 |
| Title |
HT0h_3 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Cucumis sativus |
| Characteristics |
tissue: leaf
treatment: untreated
age: Three-week-old seedlings of cucumber
|
| Treatment protocol |
Three-week-old seedlings were subjected to heat treatment at 42℃ and the leaves were collected at 0 (control), 3 and 6 h.
|
| Growth protocol |
The ‘Chinese long’ 9930，a cucumber typical of northern China, was used for expression analyses. The selected seeds after immersion and imbibition for 12h were seeded in pots containing vermiculite and matrix, and then cultivated in a growth chamber in temperature-controlled greenhouses with day and night temperature of 25 / 18 C and light cycle / dark period of 16h / 8h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After heat treatment, leaves were collected and frozen in liquid nitrogen immediately and stored at − 80 °C prior to the assays. Total RNA of each sample was isolated using the Total RNA Extractor (TRIzol) kit (B511311, Sangon, China). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Raw data of fastq format were firstly processed through perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the Cucumber (Chinese Long) v3 Genome was built using Hisat2 v2.0.5. The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Cucumber (Chinese Long) v3 Genome, http://cucurbitgenomics.org/organism/20
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
May 22, 2020 |
| Last update date |
May 23, 2020 |
| Contact name |
Zhonghai Ren |
| E-mail(s) |
[email protected]
|
| Organization name |
Shandong Agricultural University
|
| Department |
College of Horticulture Science and Engineering
|
| Lab |
State Key Laboratory of Crop Biology
|
| Street address |
Daizong Road No.61,Taian
|
| City |
Shandong |
| ZIP/Postal code |
271018 |
| Country |
China |
| |
|
| Platform ID |
GPL26594 |
| Series (1) |
| GSE151055 |
Transcriptome analysis of cucumber in response to high temperature stress |
|
| Relations |
| BioSample |
SAMN14998224 |
| SRA |
SRX8381990 |
