|
| Status |
Public on Sep 24, 2011 |
| Title |
wild-type replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
two-week-old seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
developmental stage: 2-week-old seedling
|
| Treatment protocol |
To remove any contaminating DNA, RNA was treated with DNAse.
|
| Growth protocol |
Total RNA from 2-week-old Arabidopsis thaliana (ecotype Columbia) seedlings grown on MS plates and isolated using RNeasy Plant Mini Kit from Qiagen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolation of poly (A) mRNA and preparation of cDNA library were carried out using the Illumina TrueSeq RNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
76nt reads
|
| Data processing |
TopHat 1.0.14/BowTie 0.12.5;command: tophat -a 10 -g 1 -F 0 -p 6 --segment-length=26 --segment-mismatches=2 -i 40 -I 5000 --min-coverage-intron=40 --max-coverage-intron=5000 --min-segment-intr on=40 --max-segment-intron=5000 a_thaliana arabidopsis_seedling_wt_a.fq,arabidopsis_seedling_wt_b.fq
|
| |
|
| Submission date |
Sep 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Rogers |
| E-mail(s) |
rogersma@cs.colostate.edu
|
| Organization name |
Colorado State University
|
| Department |
Computer Science
|
| Lab |
Ben-Hur
|
| Street address |
1873 Campus Delivery
|
| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80523-1873 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE32318 |
2-week-old Arabidopsis seedlings (Columbia ecotype) |
|
| Relations |
| SRA |
SRX098354 |
| BioSample |
SAMN00726687 |
