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Sample GSM1000196 Query DataSets for GSM1000196
Status Public on Dec 31, 2012
Title Col_wt
Sample type SRA
 
Source name Col_wt
Organism Arabidopsis thaliana
Characteristics cultivar: Col-0
genotype: wild type
treatment: untreated
Treatment protocol Plants were treated by 5┬ÁM estradiol with or without 1mM H2O2 for 6h in liquid 0.5 MS medium
Growth protocol Plants were grown in sterile conditions using half-stength MS culture medium (0.5 MS) containing 0.5% sucrose,
Extracted molecule total RNA
Extraction protocol Extracting total RNA made with RNeasy (Qiagen), plus AMBION DNAse treatment. Libraries were processed according to the SOLID transcriptome sequencing protocol (Publication Part Number 4452437). Briefly, total RNA was DNaseI treated and rRNA-depleted using RiboMinus Plant Kit. After the fragmentation of RNA, the 50-200nt fraction was cleaned and was the subject of adaptor hybridization and reverse transcription. The cDNA library was cleaned with Qiagen MinElute PCR purification Kit and size-selected on a 6% TBE-Urea denaturing polyacrylamide gel. The 150-250nt cDNA fraction was amplified to generate sufficient template for SOLID sequencing. To determine the accurate concentration of each library, a SOLID Library TaqMan Quantitation Kit was used according to the manufacturer's instructions. After, each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR (ePCR). ePCR beads were enriched for template-positive beads by hybridization with capture beads. Template-enriched beads were extended at the 3' end in the presence of terminal transferase and 3' bead linker. Approximately 60 million beads per sample with clonally amplified DNA were deposited onto one lane of the 5500 SOLID sequencing flowchip . The flowchip was then loaded onto a SOLID 5500xl Instrument and the 50-base sequences were obtained according to manufacturer's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB 5500xl Genetic Analyzer
 
Data processing Basecalls performed using Abi 5500xl ICS (Instrument Controller version 2011.09)
Data were filtered using the following specifications: minimum number of nucleotides in reads = 50
RNA reads were aligned to the NC_003070/NC_003070/NC_003070/NC_003070/NC_003076/NC_003076/Y08501_MT genome assembly using CLC Genomics Workbench version 4.7.2 with the configurations described in the readme.txt file on the Series record.
Calculate expression levels and discover novel exons using CLC Genomics Workbench version 4.7.2
Annotation using CLC Genomics Workbench version 4.7.2 (Data from www.geneontology.org)
Genome_build: NC_003070/NC_003070/NC_003070/NC_003070/NC_003076/NC_003076/Y08501_MT
Supplementary_files_format_and_content: Final processed data file, with min. 30 total gene reads
Supplementary_files_format_and_content: Comparing all samples (RPKM) temporary
Supplementary_files_format_and_content: Comparing all samples (RPKM) added function fields temporary
Supplementary_files_format_and_content: Comparing all samples (RPKM) added annotation from www.geneontology.org
Supplementary_files_format_and_content: Primary output from CLC Genomics Workbench version 4.7.2
 
Submission date Sep 10, 2012
Last update date May 15, 2019
Contact name Balazs Horvath
Organization name SeqOmics Biotechnology Ltd.
Department NGSP
Street address Vallalkozok u. 7.
City Morahalom
ZIP/Postal code 6782
Country Hungary
 
Platform ID GPL16033
Series (1)
GSE40735 Regulation of Oxidative Stress Responses by the Arabidopsis Heat Shock Factor A4A
Relations
SRA SRX185719
BioSample SAMN01163716

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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