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Sample GSM3905738 Query DataSets for GSM3905738
Status Public on Aug 03, 2020
Title 2D_C-3_1_miRNA-seq
Sample type SRA
 
Source name Arabidopsis ecotype Columbia (Col-0)
Organism Arabidopsis thaliana
Characteristics treatment: Non-treatment
ecotype: Columbia (Col-0)
drenched pathogen: Ralstonia solanacearum
time after pathogen drench: 2d
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the mirVana miRNA isolation kit (Ambion).
Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Data processing After TruSeq small RNA adapters were eliminated among the sequenced reads by Trimommatic software (v.0.33), the remained sequence data were mapped to the Arabidopsis genome (TAIR10) using bowtie2 (v.2.2.2).
The quantification of each miRNA was estimated using HTSeq software package.
The read counts per
million fragments mapped (CPM) of each sample were used to estimate the expression level of each gene. The CPM data were normalized by the quantile method and log2 transformation.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text format with CPM values of miRNA
 
Submission date Jun 26, 2019
Last update date Aug 03, 2020
Contact name Seon-Kyu Kim
E-mail(s) seonkyu@kribb.re.kr
Phone +82-42-879-8107
Organization name Korea Research Institutue of Bioscience & Biotechnology
Department Personalized Genomic Medicine Research Center
Street address 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
City Daejeon
ZIP/Postal code 305-806
Country South Korea
 
Platform ID GPL19580
Series (2)
GSE133321 Expression profiling by small RNA-seq for identifying miRNA associated with sound vibration in plant
GSE133325 Identifying genes associated with sound vibration in plant
Relations
BioSample SAMN12139219
SRA SRX6367448

Supplementary file Size Download File type/resource
GSM3905738_2D_C-3_1_CPM.txt.gz 2.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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