|
Status |
Public on Apr 28, 2021 |
Title |
rrp45a R1 Exp2 |
Sample type |
SRA |
|
|
Source name |
inflorescences
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype: rrp45a experiment: Experiment2
|
Growth protocol |
seeds were surface-sterilized, plated on 1xMS agar plates and 10 DAG seedlings were transferred to soil and grown in percival growth chambers with a cycle of 16 h light (21 ºC, 70% relative humidity)/ 8 h darkness (16 ºC, 70% relative humidity)
|
Extracted molecule |
total RNA |
Extraction protocol |
inflorescences were collected and snap-frozen in liquid nitrogen. Total RNA was extracted with Trizol reagent according to the instructions from the manufacturer. After the RNA extraction, the RNA was treated for polysaccharides with an additional mild EtOH precipitation. 1 µg of total RNA was used as input per sample. The libraries were constructed with the NEBNext small RNA libraries preperation kit #E7300 following the protocal of the kit. miRNA-Seq (or rather small RNA seq as you do not only sequence miRNAs)
|
|
|
Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
small RNA deseqcontrast2
|
Data processing |
trimming with cutadapt v.2.4 mapping with STAR_2.6.0a reads were quantified with featureCounts from subread-1.6.3 using an Araport11 GFF3 file modified to also include intergenic regions with a gene accession number as 1, 2, 3 etc. reads were normalized and transformed with DESeq2 DESeq2 analysis was performed and the mutant vs WT results were extracted with an alpha cut-off = 0.1 Genome_build: TAIR10 Supplementary_files_format_and_content: matrix of gathered DESeq2 contrasts from each mutant genotype vs WT
|
|
|
Submission date |
Apr 27, 2021 |
Last update date |
Apr 28, 2021 |
Contact name |
Peter Brodersen |
E-mail(s) |
pbrodersen@bio.ku.dk
|
Organization name |
University of Copenhagen
|
Department |
Department of Biology
|
Lab |
Peter Brodersen Lab
|
Street address |
Ole Maaløes Vej 5
|
City |
København N |
ZIP/Postal code |
2200 |
Country |
Denmark |
|
|
Platform ID |
GPL19580 |
Series (1) |
GSE173426 |
Nuclear and cytoplasmic RNA exosomes and PELOTA limit miRNA-induced secondary siRNA production |
|
Relations |
BioSample |
SAMN18880059 |
SRA |
SRX10687650 |