|
Status |
Public on Sep 24, 2011 |
Title |
wild-type replicate 1 |
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 |
SRX098353 |
BioSample |
SAMN00726686 |