|
| Status |
Public on Mar 28, 2013 |
| Title |
Benk_1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cultivar: Benk_1
tissue: leaf
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using the Qiagen Plant RNeasy kit (Qiagen) following the manufacturer’s instructions.
RNA-Seq libraries were prepared according to the described methods in Li, L. et al. Linking photoreceptor excitation to changes in plant architecture. Genes Dev 26, 785-790 (2012).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
Bioscope version 1.3 was used to align .csfasta and .qual files to SNP-substituted reference genomes for each accession using default parameters which allows up to 10 locations per sequenced read.
Cufflinks version 1.1 was used to quantify gene expression values using the following parameters: -F 0 –b –N –library-type fr-secondstrand –G TAIR10.gtf.
Genome_build: TAIR10
Supplementary_files_format_and_content: Expression values for all genes in the TAIR10 reference annotation as defined by Cufflinks version 1.1
|
| |
|
| Submission date |
Mar 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL14599 |
| Series (1) |
| GSE43858 |
Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq) |
|
| Relations |
| SRA |
SRX255729 |
| BioSample |
SAMN01992785 |
