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Sample GSM1664666 Query DataSets for GSM1664666
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

Supplementary file Size Download File type/resource
GSM1664666_4_miR173_dcl2dcl4.txt.gz 2.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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