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Sample GSM4148767 Query DataSets for GSM4148767
Status Public on Feb 24, 2020
Title dcl3 methylC-seq - replicate B
Sample type SRA
 
Source name inflorescence (stage 1-12) immature flower buds.
Organism Arabidopsis thaliana
Characteristics ecotype background: Columbia
genotype/variation: dcl3-1
tissue: inflorescence (stage 1-12) immature flower buds
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 genomic DNA
Extraction protocol DNA was isolated using fractional precipitation followed by phenol-chloroform extraction and RNase A treatment.
1 ug of DNA was used to prepare libraries as previously described in Urich et. al., PMID: 25692984.
Multiplexed libraries were sequenced on NextSeq 500.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
 
Description Replicate A is available in GSE79746.
Data processing Data were mapped to the TAIR10 reference genome.
MethylC-seq analyses were performed as described in Schmtiz et. al., PMID: 23739894.
Genome_build: TAIR10
Supplementary_files_format_and_content: allC files reporting methylation of each cytosine in the genome is provided for methylC-seq data.
 
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 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 SAMN13192919
SRA SRX7099477

Supplementary file Size Download File type/resource
GSM4148767_allC_dcl3_RepB.tsv.gz 184.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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