|
| Status |
Public on May 31, 2012 |
| Title |
At_mRNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Rosette leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Landsberg erecta
Stage: before bolting
ploidy: autotetraploids
sample: Rosette leaves
age: 3-4 weeks old
|
| Growth protocol |
All plants were grown under a 16/8-hour light/dark cycle with temperatures of 22C (light) and 20C (dark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mature leaves (3-4 weeks old A. thaliana; 6-7 weeks old A. arenosa or allotetraploids plants) prior to bolting using plant RNA purification reagent (Invitrogen, Carlsbad, CA). The integrity of extracted RNA was verified by resolving 1ug RNA in an 1% formaldehyde denaturing agarose gel. An aliquot of 10ug total RNA was used to prepare mRNA-seq libraries using Illumina mRNA-seq sample preparation kit (Illumina Inc., San Diego, CA). Libraries with a range of 200-25 bp were excised and amplified for subsequent cluster generation and massively parallel sequencing using the Illumina Genome Analyzer with read lengths ranged from 60 to 83 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Illumina mRNA-seq
|
| Data processing |
Alignment: mRNA-seq reads each were mapped to TAIR9 genome and cDNA sequence using BFAST software (http://bfast.sourceforge.net)
|
| |
|
| Submission date |
Jun 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Z Jeffrey Jeffrey Chen |
| E-mail(s) |
[email protected]
|
| Phone |
512-475-9327
|
| Organization name |
The University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Lab |
Polyploidy, Hybrid Vigor, and Epigenetics
|
| Street address |
2506 Speedway NMS 3.122 Stop A500
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712-1597 |
| Country |
USA |
| |
|
| Platform ID |
GPL9062 |
| Series (1) |
| GSE29687 |
Cis- and trans- regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids |
|
| Relations |
| SRA |
SRX076018 |
| BioSample |
SAMN00626994 |
