|
| Status |
Public on Mar 28, 2013 |
| Title |
CG_103.17 |
| Sample type |
SRA |
| |
|
| Source name |
leaf tissue
|
| Organism |
Capsella grandiflora |
| Characteristics |
tissue: leaf tissue
developmental stage: maturing leaves
|
| Growth protocol |
Standardized greenhouse conditions
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen Rneasy Plant Mini kit, standard protocol
Standard Illumina paired-end mRNA seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
C. grandiflora grown from wild-collected seed from Pili, Greece
|
| Data processing |
Illumina flourescence data was processed through the illumina analysis Pipeline for basecalling and quality assignment
For flowerbud samples, illumina fastq quality scores were converted to PHRED+33, leaf samples were retained at the PHRED+64 format
Reads were aligned to the Capsella reference genome using bowtie. The initial release JGI Maker gene models were used to assign expresion using the tophat-cufflinks pipeline including the data normalization option to generate expression FPKM: fragments per Kilobase of exon per million reads.
Genome_build: Capsella Rubella v1 (also listed as 183), http://www.phytozome.org/dataUsagePolicy.php?org=Org_Crubella
Supplementary_files_format_and_content: TAB delimitted single sample FPKM expression reads, gene models are descibed here ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Crubella/annotation/Crubella_183_gene.gff3.gz
|
| |
|
| Submission date |
Mar 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Wright |
| E-mail(s) |
stephen.wright@utoronto.ca
|
| Organization name |
University of Toronto
|
| Department |
Department of Ecology and Evolutionary Biology
|
| Lab |
Wright Laboratory
|
| Street address |
25 Willcocks Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S 3B2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16879 |
| Series (2) |
| GSE45518 |
The consequences of rapid mating system evolution in crucifer genomes |
| GSE45687 |
The Capsella rubella genome and the genomic consequences of rapid mating system evolution |
|
| Relations |
| SRA |
SRX255499 |
| BioSample |
SAMN01992702 |
