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Sample GSM954178 Query DataSets for GSM954178
Status Public on Jul 13, 2017
Title wild-type under control
Sample type SRA
 
Source name wild-type
Organism Arabidopsis thaliana
Characteristics genotype/variation: wild-type
stress: none
Treatment protocol Two-week-old plants were subjected to drought stress treatment as described previously (Matsui et al. 2008, Plant Cell Physiol, 49: 1135-1149).
Growth protocol Arabidopsis rdr1/2/6 and wild-type plants were grown on MS medium at 22 ºC in the cycle of 16hr light / 8hr dark condition for 2 weeks as described previously (Matsui et al. 2008, Plant Cell Physiol, 49: 1135-1149).
Extracted molecule total RNA
Extraction protocol smRNAs were extracted from plants using mirVana miRNA Isolation Kit (Life Technologies). smRNA libraries for SOLiD sequencing were constructed according to the protocol of SOLiD Total RNA-Seq Kit (Life Technologies). First, smRNAs were ligated with 5’ adapter and 3’ adapter to generate cDNAs. cDNAs were separated in 8M urea, 7.5% acrylamide gel and 60-80 nt cDNAs were recovered. The cDNAs were amplified by 12-15 cycles of PCR using barcode primers (Life technologies) and subjected to SOLiD sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD 4 System
 
Data processing Adaptor sequences (downstream of 26 nt color code) were eliminated from the SOLiD sequence data. They were mapped on Arabidopsis genome, using bowtie software (Langmead et al., 2009). We used the following two-step normalization for data analysis of smRNAs. 1) smRNAs mapped on annotated genes were counted and normalized independently for rdr1/2/6 and WT by adjusting a slope of linear approximate equation between control and drought stress conditions. We used top 10% highly-expressed smRNA loci for the normalization. 2) We used tag numbers mapped on miRNA loci by adjusting a slope of linear approximate equation between rdr1/2/6 and WT, because accumulation of miRNAs is thought to be less affected by loss of RDR1/2/6.
Genome_build: TAIR10 Arabidopsis genome annotation was used.
Supplementary_files_format_and_content: Tag no. was displayed as variablestep in wiggle (WIG) format file. The position of AGI-annotated genes was shown in BED file.
 
Submission date Jun 29, 2012
Last update date May 15, 2019
Contact name Motoaki Seki
E-mail(s) motoaki.seki@riken.jp
Organization name RIKEN CSRS
Street address 1-7-22, Suehiro-cho, Tsurumi
City Yokohama
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL14599
Series (2)
GSE39024 Deep sequencing of small RNAs
GSE39037 Deep sequencing of small and uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants
Relations
SRA SRX157445
BioSample SAMN01085313

Supplementary file Size Download File type/resource
GSM954178_smRNA_WT_Con_Minus.wig.gz 8.4 Mb (ftp)(http) WIG
GSM954178_smRNA_WT_Con_Plus.wig.gz 8.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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