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Sample GSM852801 Query DataSets for GSM852801
Status Public on May 03, 2012
Title xrn2-1xrn4-6 replicate 2
Sample type SRA
 
Source name 2-week-old xrn2-1xrn4-6 seedlings
Organism Arabidopsis thaliana
Characteristics condition: grown on LS plate
age: 2-week-old
ecotype: Columbia
rna fraction: polyA RNA
genotype/variation: xrn2-1xrn4-6 plants
Growth protocol Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes containing LS agar (0.85%) medium supplemented with 1% sucrose for 2 weeks or on soil for 3 weeks under 16-h-light/8-h-dark.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the plants using Trizol reagent (Invitrogen, Carlsbad, CA). Poly(A)+ fraction was separated from 80 μg of total RNA using Oligotex mRNA Mini Kit (Qiagen, Valencia, CA) and fragmented using Fragmentation Reagents (Applied Biosystems/Ambion, Austin, TX) at 70°C for 15 min. Fifty nanograms of the fragmented RNA was used to generate strand-specific RNA-Seq library according to the Directional mRNA-Seq Library Preparation Protocol (Illumina). RNA-Seq libraries were sequenced for 42 cycles using the Illumina Genome Analyser II (wild type and fry1-6) or for 50 cycles using the HiSeq 2000 (xrn3-3, xrn3-3xrn4-6, 3-week-old wild type and xrn2-1xrn3-3) according to manufacturer’s instruction. Image analysis and base calling were performed with the standard Illumina pipeline. Read sequences were aligned with the Tophat software to the TAIR9 reference genome (Trapnell et al. 2009).
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description biological replicate 2
Data processing Read sequences were aligned with the Tophat software to the TAIR9 reference genome
 
Submission date Dec 22, 2011
Last update date May 15, 2019
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL13222
Series (1)
GSE34654 Genome-wide identification of non-coding RNAs targeted by XRN exoribonucleases in collaboration with FRY1 using RNA-Seq in Arabidopsis thaliana.
Relations
SRA SRX113693
BioSample SAMN00769269

Supplementary file Size Download File type/resource
GSM852801.sam.gz 1.2 Gb (ftp)(http) SAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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