|
Status |
Public on Apr 13, 2020 |
Title |
dcl4_MS_smRNA_rep3 |
Sample type |
SRA |
|
|
Source name |
dcl4-2 seedlings on MS medium
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype: dcl4-2 tissue: whole seedling age: 14-day-old plant growth: grown on MS 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 |
SAMN14586929 |
SRA |
SRX8109859 |