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Sample GSM1239085 Query DataSets for GSM1239085
Status Public on Mar 05, 2014
Title ibl1 mutant #1
Sample type SRA
 
Source name ibl1 mutant
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype/variation: ibl1-/ibl1-
tissue: 10d-old seedling
Treatment protocol no treatment
Growth protocol Arabidopsis thaliana plants (ecotype Col-0) were grown at 22°C and a 16-h photoperiod (65 μE m−2 s−1) on half-strength MS medium and 0.7 % plant tissue culture agar. Entire seedlings were collected at 10 days after sawing.
Extracted molecule polyA RNA
Extraction protocol Three independent biological replicates were done. Total RNA was extracted using the RNeasy plant mini kit followed by DNaseI treatment (Qiagen). The RNA was subjected to DNaseI (Promega) treatment and tested by PCR to ensure no genomic DNA contamination. The preparation of mRNA-Seq libraries with bilogical duplicates was performed according to instructions from the Illumina mRNA-Seq sample preparation kit (15008136 Illumina).
According to manufactor's instruction (Illumina TruSeq RNA kit Part # 15008136 Rev. A)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample 7
Data processing CASAVA version 1.8.2 was used to generate fastq files and demultiplexing.
RNA-seq reads were aligned to the Arabidopsis thaliana genome assembly version TAIR10 using TopHat version 1.4.1 using the gff file version for TAIR10
Alignment files were compared for differential gene expression using the Cuffdiff option of the Cufflink program (version 1.0.3)
Genome_build: Arabidopsis thaliana genome assembly version TAIR10
Supplementary_files_format_and_content: gene_exp.diff are tabulator delimiter files generated with Cuffdiff. genes.fpkm_tracking tracks the summed FPKM of transcripts sharing each gene_id and gene_exp.dif tracks the results of tests
 
Submission date Sep 24, 2013
Last update date May 15, 2019
Contact name Kengo Morohashi
E-mail(s) morohashi.1@osu.edu
Phone 614-688-4954
Organization name The Ohio State University
Department Molecular Genetics
Lab Erich Grotewold
Street address 1060 Carmack Rd
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
 
Platform ID GPL13222
Series (2)
GSE51119 A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal [RNA-seq]
GSE51121 A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal
Relations
BioSample SAMN02363366
SRA SRX359421

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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