|
| Status |
Public on Apr 13, 2020 |
| Title |
dcl4dcl2_ABA_smRNA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
dcl4-2 dcl2-1 seedlings on ABA medium
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: dcl4-2 dcl2-1
tissue: whole seedling
age: 14-day-old plant
growth: grown on MS+1 μM ABA medium
|
| Treatment protocol |
No treatment
|
| Growth protocol |
plants were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts of 20-day-old were collected for small RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy mini kit(Qiagen)
NEBNext® Small RNA Library Prep Set for Illumina
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence reads were filtered and then mapped to TAIR10 genome using Bowtie-1.2.2 with following parameters: -v 0 -a -M 3 --best --strata
22-nt small RNA read were selected using samtools v1.9
Tags Per Million (TPM) were calculated and differential 21- and 22-nt siRNA production genes were called out using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include TPM values for each sample, the log2(FoldChange) value and the according p-value of pair-comparisons
|
| |
|
| Submission date |
Apr 12, 2020 |
| Last update date |
Apr 15, 2020 |
| Contact name |
Bosheng Li |
| E-mail(s) |
libs@sustc.edu.cn
|
| Organization name |
SUSTC (current, may different with previous institution )
|
| Department |
MCDB
|
| Street address |
SUStech Huiyuan #1 406
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
581055 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE136164 |
Plant 22-nt siRNAs mediate translational repression and stress adaptation |
| GSE148513 |
22-nucleotide siRNAs mediate translational repression and trigger a silencing storm |
|
| Relations |
| BioSample |
SAMN14586916 |
| SRA |
SRX8109870 |
