|
| Status |
Public on Apr 02, 2013 |
| Title |
Arabidopsis lyrata MN47 floral bud 12, biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
floral bud stage 12
|
| Organism |
Arabidopsis lyrata |
| Characteristics |
strain: MN47
tissue: flowers
developmental stage: floral bud stage 12
|
| Growth protocol |
Plants were grown in Percival AR66L growth chambers under 16 hours of light and 8 hours of dark. Floral buds were collected at stage 12 for RNA preparation. The floral tissue collection methods are as reported by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was frozen in liquid nitrogen, ground to a fine power in liquid nitrogen, and RNA was extracted with the Plant Reagent (Invitrogen using the manufacturer's recommendations). Specific details are as given in Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
Illumina non-strand-specific (a minor adaptation of the Illumina mRNA-seq methods as reported by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Alyr_MN47_br_1
PolyA RNA.
Barcode for sample: GTAT
|
| Data processing |
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol and base calling was performed with the Illumina version SCS2.6 software. For the "Real Time Analysis (RTA)" that is implemented in the SCS control software, we used "per lane" parameters for basecalling.
Barcode splitting was performed as described by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with tophat 1.3.1 and cufflinks 0.9.2.
Genome_build: Alyrata_107 ('Alyrata_107.fa', which is the nucleotide FASTA format file of the genomic assembly, and 'Alyrata_107_cds.fa', which is the nucleotide FASTA format file of all gene-coding sequences, were downloaded from Phytozome at http://www.phytozome.net/ ). This genome build is as published by Hu et al. 2011. Nat. Genet. 43(5):476-81.
Supplementary_files_format_and_content: A single tab-delimited text file per sample with gene ids and FPKM values.
|
| |
|
| Submission date |
Apr 01, 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 |
GPL16940 |
| Series (2) |
| GSE45676 |
Understanding transcriptional changes associated with the transition to selfing in Arabidopsis thaliana by using outgroup data |
| GSE45687 |
The Capsella rubella genome and the genomic consequences of rapid mating system evolution |
|
| Relations |
| SRA |
SRX257635 |
| BioSample |
SAMN01995760 |
