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Sample GSM2829922 Query DataSets for GSM2829922
Status Public on Dec 31, 2017
Title mir845 1n rep1
Sample type SRA
Source name Pollen
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: Pollen
Growth protocol Plants were grown under long day conditions at 22 °C. Seeds were always surface sterilized with sodium hypochlorite, sowed on Murashige and Skoog (MS) medium and stratified for 3 days at 4ºC. Seedlings were transplanted to soil two weeks after germination and grown under long day conditions at 22 °C.
Extracted molecule total RNA
Extraction protocol Flowers were harvested in a beaker, covered with 9% sucrose solution and shaken vigorously for 5min to release pollen grains into the solution. The subsequent centrifugation- and filtering-steps were carried out in 9% sucrose solution. Total RNA was extracted using Trizol reagent (Ambion/ Life Technologies, USA) and glass beads (1.25-1.55 mm; Carl Roth).
10 μg of total RNA were run on a 14% TBE UREA Polyacrylamide gel for size selection. Gel slices containing RNA in the range of 17- to 25-nt were purified following the Illumina TrueSeq small RNA protocol for gel extraction. Libraries were constructed using the Illumina TruSeq Small RNA library preparation kit according to the manufacturer’s instructions.
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
Description Small RNA
Data processing Reads were pre-processed by trimming the 3’ adapter and filtering collapsed reads according to length and quality.
Filtered reads were mapped to the Arabidopsis TAIR10 genome annotation with bowtie reporting all multi-mappers.
Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features
Submission date Oct 24, 2017
Last update date May 15, 2019
Contact name Filipe Borges
Organization name Institut Jean-Pierre Bourgin - INRAE
Street address Route de St-Cyr (RD10)
City Versailles
ZIP/Postal code 78026
Country France
Platform ID GPL17639
Series (2)
GSE106115 microRNA-triggered transposon small RNAs mediate genome dosage response (mir845 sRNA-Seq)
GSE106117 microRNA-triggered transposon small RNAs mediate genome dosage response
BioSample SAMN07830391
SRA SRX3318200

Supplementary file Size Download File type/resource
GSM2829922_miR845_1n_rep1_pollen.txt.gz 10.8 Mb (ftp)(http) TXT
GSM2829922_miR845_1n_rep1_pollen_tair10.txt.gz 543.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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