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Sample GSM3954871 Query DataSets for GSM3954871
Status Public on Jul 01, 2020
Title At.TRIzol.total.R1
Sample type SRA
 
Source name At.inflorescence.TRIzol.total
Organism Arabidopsis thaliana
Characteristics tissue: inflorescence
library preparation: TruSeq
rna isolation: TRIzol
molecule subtype: small RNA
Extracted molecule total RNA
Extraction protocol RNA was extracted with the standard TRIzol method or with the TRaPR isolation method.
Libraries were prepared with from TRIzol or TRaPR isolated RNA with the TRUseq or Lexogen sRNA library preparation kits or with a custom library preparation protocol.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Description processed data file: At_miRNA_counts.csv
Data processing Illumina Casava1.8 software used for basecalling.
Trimming of reads with Trimmomatic 0.36
Mapping to the Arabidopsis thaliana genome (TAIR10) with Bowtie 1.2.1.1
Mapping to the Drosophila melanogaster genome (BDGP6) with Bowtie 1.2.1.1
Mapping to the Mus musculus genome (GRCm38) with Bowtie 1.2.1.1
Read counting to miRBase annotation with Rsubread 1.26.1
Read normalization with DEseq2.
Genome_build: TAIR10
Genome_build: BDGP6
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated text files of library and log2 normalized miRNA read counts
 
Submission date Jul 18, 2019
Last update date Jul 01, 2020
Contact name Stefan Oberlin
E-mail(s) stefan.oberlin@ucsf.edu
Organization name ETH Zürich
Department Department of Biology
Street address Universitätstrasse 2
City Zürich
ZIP/Postal code 8092
Country Switzerland
 
Platform ID GPL19580
Series (1)
GSE134516 A universal, benchtop, gel-free method for the rapid and simultaneous isolation of all known classes of functional small RNAs
Relations
BioSample SAMN12317561
SRA SRX6470264

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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