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Sample GSM3913300 Query DataSets for GSM3913300
Status Public on Feb 24, 2020
Title dcl1 sRNA
Sample type SRA
 
Source name inflorescence (stage 1-12) immature flower buds
Organism Arabidopsis thaliana
Characteristics genotype/variation: dcl1-9
tissue: inflorescence (stage 1-12) immature flower buds
ecotype: Columbia
Growth protocol Plants were grown under 16-hour day conditions at 22ÂșC in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds.
Extracted molecule total RNA
Extraction protocol Inflorescence small RNA was isolated with TRIzol reagent (Invitrogen) and concentrated using the mirVana microRNA Isolation Kit (Ambion).
For AGO1-IP samples, AGO1 was immunoprecipitated from inflorescence tissue using Agrisera anti-AGO1 primary antibody. RNA was isolated from AGO1-IP or mock-IP samples using TRIzol reagent.
Size-enriched small RNAs were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina).
Multiplexed libraries were sequenced on HiSeq2500 or HiSeq4000.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Description total small RNA
Data processing Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
ShortStack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.
 
Submission date Jul 01, 2019
Last update date Feb 24, 2020
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 GPL19580
Series (1)
GSE133618 Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes
Relations
BioSample SAMN12173466
SRA SRX6385956

Supplementary file Size Download File type/resource
GSM3913300_dcl1-9_normalizedCounts.tsv.gz 11.7 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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