|
| Status |
Public on Jul 12, 2012 |
| Title |
mRNA from DEX-treated 35S:GR-RBE floral buds, biological replicate 2, 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 |
SRX129188 |
| BioSample |
SAMN00811246 |
