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Sample GSM894356 Query DataSets for GSM894356
Status Public on Jul 12, 2012
Title mRNA from DEX-treated 35S:GR-RBE floral buds, biological replicate 1, techinical replicate 2
Sample type SRA
 
Source name floral buds, DEX-treated 35S:GR-RBE
Organism Arabidopsis thaliana
Characteristics strain: L er with 35S:GR-RBE transgene
tissue: floral buds
developmental stage: mixed stages
Treatment protocol Floral buds were treated with DEX (10uM dexamethasone, 0.1% ethanol, 0.015% silwet) or mock (0.1% ethanol, 0.015% silwet) for four hours.
Growth protocol Plants were grown at 22°C under 16-hour light/ 8-hour dark conditions
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol (Invitrogen), treated with TURBO DNase (Applied Biosystems), purified using the Rneasy kit (Qiagen). Libraries were produced according to the standard Illumina protocols.Briefly, poly-A containing mRNA molecules were first purified from total RNA using poly-T attached magnetic beads and fragmented into small pieces using divalent cations. cDNA was synthesized from the fragmented mRNA, ligated with adapters and purified by Gel Extraction Kit (Qiagen). cDNA samples were amplified by PCR and purified with PCR purification Kit (Qiagen). Purified amplicons were run on an Illumina Genome Analyzer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing We used Tophat v1.2.0 (Trapnell et al. 2009) to perform spliced alignments of the reads against the Arabidopsis thaliana TAIR10 reference genome. Only reads that mapped to a single unique location with in the genome with a maximum of two mismatches in the anchor region of the spliced alignment were reported in these results. We used the default settings for all other Tophat options. To obtain a tally of the number of the reads that overlapped the exons of a gene, we analyzed the aligned reads with HTSeq v0.4.5p6 and the gene structure annotation file for the reference genome (TAIR10). The tally for each sample was then processed with LOX v1.6 (Zhang et al. 2010) to statistically analyze the gene expression levels.
 
Submission date Mar 13, 2012
Last update date May 15, 2019
Contact name Francesc Lopez
E-mail(s) francesc.lopez@yale.edu
Organization name Yale University
Department Department of Genetics
Lab YCGA
Street address P.O. Box 27386
City West Haven
State/province CT
ZIP/Postal code 06516
Country USA
 
Platform ID GPL13222
Series (1)
GSE36469 High-thoughput Illumina RNA sequencing to identify downstream target genes of RABBIT EARS (RBE) in the flowers of Arabidopsis thaliana
Relations
SRA SRX129186
BioSample SAMN00811244

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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