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Sample GSM1183036 Query DataSets for GSM1183036
Status Public on Jan 01, 2014
Title Col-0/control
Sample type SRA
 
Source name control seedlings, 36 hours
Organism Arabidopsis thaliana
Characteristics tissue: seedling
genotype/variation: Col-0 wild type
Growth protocol ZFP3 overexpressing and Col-0 wild type seeds were germinated on media supplemented with 5µM estradiol or 5µM estradiol and 2.5µM ABA. Seedlings on estradiol containing media were harvested after 36 hours and seedlings germinated in the presence of ABA and estradiol were harvested after 84 hours to obtain seedlings in physiologically identical radical stage for both conditions.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with Qiagen Plant RNeasy Kit, followed by DNaseI treatment using Ambion's TURBO DNA-free™ kit. RNA quality and quantity measurements were performed on Bioanalyzer (Agilent Technologies).
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 Solid 4+ ICS (Instrument Controller version 2010.04)
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 5.5.1 with the following configurations…*
Calculate expression levels and discover novel exons using CLC Genomics Workbench version 5.5.1
Annotation using CLC Genomics Workbench version 5.5.1 (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: Text file with expression values (Read Per Kilobase of exon Model value)
 
Submission date Jul 10, 2013
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)
GSE48661 The Arabidopsis Zinc Finger Protein 3 integrates ABA and light signaling in seed germination and plant development
Relations
BioSample SAMN02230332
SRA SRX319496

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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