|
Status |
Public on Mar 24, 2016 |
Title |
pollen of dcl2/dcl4 with the transgene KRP6pro::miR173site-trGFP |
Sample type |
SRA |
|
|
Source name |
mutant_miR173site-trGFP_pollen
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype background: Columbia-0 genotype/variation: dcl2/dcl4 mutant transgene: KRP6pro::miR173site-trGFP tissue: mature pollen molecule subtype: small RNA
|
Treatment protocol |
Mature pollen was harvested in the morning following anthesis.
|
Growth protocol |
Plants were grown on soil in 18 hour long days at 22C. All plants were grown side-by-side.
|
Extracted molecule |
total RNA |
Extraction protocol |
Mature pollen was harvested by manual collection of open flowers into a 18% sucrose collection buffer placed on ice. Tubes containing the extraction buffer and open flowers were vortexed for 5 minutes and centrifuged for 3 minutes at 3,000 rpm in a centrifuge equipped with a tilt rotor. Pollen RNA was extracted with TRIzol reagent according to manufacturer instructions. Small RNA was enriched by cutting the 17-29nt small RNA fraction from a polyacrylamide gel and subsequent elution and precipitation. Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit
|
|
|
Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
4-pGMA149:KRP6pro::miR173site-trGFP_dcl2dcl4
|
Data processing |
Illumina Casava1.7 software was used for basecalling.
Sequenced reads de-multiplexed and were trimmed for adaptor sequence
Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, only genome matching reads retained (UEA small RNA tool v 2.5.0 used)
tRNA and rRNA-matching reads were removed
Genome_build: TAIR10
Supplementary_files_format_and_content: genome-matched and filtered small RNA sequences and the number of times they were sequenced
|
|
|
Submission date |
Apr 22, 2015 |
Last update date |
May 15, 2019 |
Contact name |
R. Keith Slotkin |
E-mail(s) |
kslotkin@danforthcenter.org
|
Organization name |
Donald Danforth Plant Science Center
|
Street address |
975 North Warson Road
|
City |
St. Louis |
State/province |
Missouri |
ZIP/Postal code |
63132 |
Country |
USA |
|
|
Platform ID |
GPL17639 |
Series (1) |
GSE68154 |
Transitive silencing of mobile small RNAs in Arabidopsis Pollen |
|
Relations |
BioSample |
SAMN03497820 |
SRA |
SRX1004262 |