|
| Status |
Public on May 19, 2015 |
| Title |
As_mRNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Rosette leaves
|
| Organism |
Arabidopsis suecica |
| Characteristics |
Stage: before bolting
ploidy: allotetraploids
|
| Growth protocol |
All plants were grown under a 16/8-hour light/dark cycle with temperatures of 22oC (light) and 20oC (dark).
|
| Extracted molecule |
polyA 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 1 µg RNA in an 1% formaldehyde denaturing agarose gel. An aliquot of 10 µg 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 200bp} 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 HiSeq 2000 |
| |
|
| Description |
Illumina mRNA-seq
|
| Data processing |
mRNA-seq reads were aligned to TAIR9 genome and cDNA sequence using BFAST-0.7.0a
Transcript levels were quantified by counting Reads Per Kilobase of exon model per Million mapped reads (RPKM)
Allelic expression was identified by assigning the reads in an allotetraploids into A. thaliana and A. arenosa reads using two or more distinct SNPs between A. thaliana and A. arenosa.
Genome_build: TAIR9 genome and cDNA sequence
Supplementary_files_format_and_content: matrix listing of transcripts and RPKM
|
| |
|
| Submission date |
Sep 09, 2013 |
| 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 |
GPL17708 |
| Series (1) |
| GSE50715 |
Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids |
|
| Relations |
| BioSample |
SAMN02351556 |
| SRA |
SRX347365 |
