|
| Status |
Public on Mar 05, 2014 |
| Title |
Col #1 |
| Sample type |
SRA |
| |
|
| Source name |
Col
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: +/+
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 9
|
| 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 |
SAMN02363360 |
| SRA |
SRX359423 |
