|
| Status |
Public on Apr 13, 2020 |
| Title |
RNAi-2 |
| Sample type |
SRA |
| |
|
| Source name |
axillary bud
|
| Organism |
Cucumis sativus |
| Characteristics |
age: two-month old plant
tissue: lateral bud
genotype: CsBRC1-RNAi
|
| Treatment protocol |
A 585-bp specific fragment of the CsBRC1 coding sequence was used for generating the CsBRC1-RNAi construct and the empty PFGC-1008 vector was used as transformation control. The recombinant construct was introduced into Agrobacterium strain GV3101 and transformed into cucumber inbred line R1461.
|
| Growth protocol |
The cucumber seeds were germinated at 28°C in dark and then grown in a growth chamber at 16h day (25°C) and 8h night (18°C) until two true-leaf stage. Seedlings were then transferred to the greenhouse of China Agricultural University in Beijing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The lateral buds from the same node of WT and transgenic cucumber plants were collected for RNA-seq analysis,and RNA was isolated with Transzol reagent.
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 |
| |
|
| Description |
The lateral buds from the same node of WT and transgenic cucumber plants were collected for RNA-seq analysis.
|
| 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 (ftp://cucurbitgenomics.org/pub/cucurbit/genome/cucumber/Chinese_long/) using HISAT. 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 CPM (counts 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 CPM(counts per Million) values for 4 Samples .
|
| |
|
| Submission date |
Dec 17, 2018 |
| Last update date |
Apr 13, 2020 |
| Contact name |
Renyi Liu |
| E-mail(s) |
[email protected]
|
| Phone |
02157078228
|
| Organization name |
Shanghai Center for Plant Stress Biology
|
| Department |
Bioinformatics
|
| Street address |
3888 Chenhua Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL16310 |
| Series (1) |
| GSE123949 |
CsBRC1 inhibits axillary bud outgrowth by repressing auxin efflux carriers CsPIN1b and CsPIN3 and in response to shade in cucumber |
|
| Relations |
| BioSample |
SAMN10602942 |
| SRA |
SRX5141076 |
