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Sample GSM2829911 Query DataSets for GSM2829911
Status Public on Dec 31, 2017
Title ler_292304
Sample type SRA
 
Source name Pollen
Organism Arabidopsis thaliana
Characteristics ecotype: Ler-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 2-3 days at 4ºC. Seedling were transplanted to soil 2 weeks after germination.
Extracted molecule total RNA
Extraction protocol Pollen was collected in 1.5mL eppendorf tubes by vortexing open flowers in pollen extraction buffer (PEB, 10 mM CaCl2, 2 mM MES, 1 mM KCl, 1% H3BO3, 10% Sucrose, pH 7.5) for 3 min (31), followed by filtration through a 30um mesh (Partec/Sysmex) and centrifugation at 5,000g for 1 min. Pollen was suspended in 50ul of PEB, immediately frozen in liquid nitrogen and stored at -80ºC until further use.
Libraries for RNA sequencing from Col-0 and Ler-0 pollen were prepared using rRNA-depleted total RNA samples and the ScriptSeq-v2 RNA-Seq Library Prep kit (Epicenter/Illumina), following manufacturer instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing FastQ files were processed and mapped to TAIR10 genome using SubRead, normalized by calculating the number of paired-end reads per kilobase of transcript per million of mapped reads (FPKM), and analyzed using R scripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt file with FPKM counts
 
Submission date Oct 24, 2017
Last update date May 15, 2019
Contact name Filipe Borges
E-mail(s) filipe.borges@inrae.fr
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)
GSE106113 microRNA-triggered transposon small RNAs mediate genome dosage response (RNA-Seq)
GSE106117 microRNA-triggered transposon small RNAs mediate genome dosage response
Relations
BioSample SAMN07830379
SRA SRX3318189

Supplementary file Size Download File type/resource
GSM2829911_Ler_pollen_tair10_FPKM.txt.gz 674.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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