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Sample GSM4148764 Query DataSets for GSM4148764
Status Public on Feb 24, 2020
Title pol IV sRNA - replicate B
Sample type SRA
 
Source name inflorescence (stage 1-12) immature flower buds
Organism Arabidopsis thaliana
Characteristics ecotype background: Columbia
genotype/variation: nrpd1a-3 (SALK_128428)
tissue: inflorescence (stage 1-12) immature flower buds
molecule subtype: small RNA
Growth protocol Plants were grown under 16-hour day conditions at 22ยบC 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 HiSeq 4000
 
Description total small RNA.
Replicate A in GSE118705.
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 genome-mapped small-RNA read.
 
Submission date Nov 04, 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 GPL21785
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 SAMN13192922
SRA SRX7099474

Supplementary file Size Download File type/resource
GSM4148764_pol4_RepB_normalizedCounts.tsv.gz 2.7 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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