|
| Status |
Public on Jun 22, 2016 |
| Title |
WT.0.3 |
| Sample type |
SRA |
| |
|
| Source name |
Wild-type seedling, 0 mins, rep 3
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype/variation: wild-type
treatment: estrogen
time: 0 mins
tissue: seedling
|
| Treatment protocol |
After seven days of growth, estrogen was added to a final concentration of five microMolar to each flask. Plants were quickfrozen in liquid nitrogen 0, 60 and 120 minutes after addition of estrogen.
|
| Growth protocol |
Seeds were surface sterilized in bleach and rinsed multiple times in sterile water. Following two days of stratification at 4 degrees in the dark,50 seeds each were transferred to 250 ml ehrlenmeyer flasks containing 50 mls of sterile MS medium and capped loosely with aluminum foil. Flasks were swirled gently on a platform shaker placed under a bank of cool white fluorescent lamps.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissue was ground to a fine powder in liquid nitrogen and mRNA was extracted using Quiagen's RNEasy kit.
oligo dT primed cDNA was used as the basis for a library made using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
OtA3009
Col wild-type
|
| Data processing |
Alignment to genome, TopHat v2.0.10, --no-novel-juncs
Transcript abundances, Cufflinks
Merge transcript abundances, Cuffmerge
Determine differential expression, Cufflinks
Genome_build: TAIR10
Supplementary_files_format_and_content: Normalized FPKM abundance measurements generated by Cufflinks are reported in Barton-ESTAIG1.series_matrix.txt.
|
| |
|
| Submission date |
Jun 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Samuel Hokin |
| E-mail(s) |
shokin@carnegiescience.edu
|
| Phone |
608-663-8920
|
| Organization name |
Carnegie Institution for Science
|
| Department |
Plant Biology
|
| Lab |
Barton Lab
|
| Street address |
260 Panama St
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE70100 |
Identification of mRNAs Regulated in Response to Transcriptional Activation of the Arabidopsis ABA INSENSITIVE GROWTH 1 (ABIG1) Transcription Factor cDNA |
|
| Relations |
| BioSample |
SAMN03784954 |
| SRA |
SRX1067797 |
