|
| Status |
Public on Apr 15, 2013 |
| Title |
RVE8:GR_mock_2 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 7 days old
tissue: whole seedlings
genotype/variation: rve8-1 RVE8::RVE8:GR
treatment: mock
|
| Treatment protocol |
At ZT4 (4 hourse after lights on), meshes with the seedlings were transferred to liquid MS+3% sucrose media containing 30 mM dexamethasone (DEX) or the same volume of solvent (mock). After four hours incubation with gentle agitation, plants were harvested and quickly frozn in liquid nitrogen.
|
| Growth protocol |
Arabidopiss rve8-1 RVE8::RVE8:GR and rve8-1 seeds (~30 seeds/ per sample) were sterilized and stratified on fine nylon mesh on MS +3% sucrose at 4 degree in the dark for 2 days. Seedlings were grown in 12 hours light (~50 micro Ei white light)/ 12 hours dark for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using trizol and then purified by Qiagen mini-elute column. A customized Illumina-based strand-specific multiplex library construction protocol was used (modified from Wang et al., A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq, 2011)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 5
|
| Data processing |
Illumina Casava version 1.8 was used for basecalling.
Quality filtering (-q 20 -p 85, minimum quality score to keep: 20, minimum percent of bases that must satify the quality score cut-off: 85) using FASTX-toolkit (command-line)
Remove adaptor contamination using a perl script
De-multiplexing (allow one mis-match in the index sequnce) using "FASTX Barcode Splitter" included in FASTX-toolkit and removed the index sequnce from the reads
The reads were mapped to Arabidopsis cDNA representative_gene_model (TAIR 10) using BWA (aln -l 20, -t 4, using the first 20 subsequnce as seeds, tread number: 4)
Used samtools to combine bam files from the two lanes together and convert to sam files
Separated the reads mapped to forward or reverse strands using command-line
Summarized from the sam files to counts using R
Genome_build: TAIR10 cDNA representative_gene_model
Supplementary_files_format_and_content: sam2counts_RV.txt: COUNTS from reads mapped to the reversed strand in the 12 samples; suitable for edgeR analysis
|
| |
|
| Submission date |
Jun 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Polly Yingshan Hsu |
| Organization name |
Duke University
|
| Department |
Biology
|
| Lab |
Philip Benfey
|
| Street address |
Duke University
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE38879 |
Identification of RVE8 target genes |
|
| Relations |
| SRA |
SRX155666 |
| BioSample |
SAMN01057261 |
