|
| Status |
Public on Mar 02, 2015 |
| Title |
Sample5_ColA9xAa_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis seeds
|
| Organism |
Arabidopsis thaliana x Arabidopsis arenosa |
| Characteristics |
ecotype: A. thaliana eco. ColA9 X A. arenosa eco. Strecno
tissue: whole seeds
time: 3 days after pollination
|
| Treatment protocol |
Seeds were harvested fresh from ColA9 X C24 and C24A9 X Col-0 and frozen on dry ice. RNA isolation using Invitrogen's Plant RNA Reagent was described by Burkart-Waco et al. (2013).
|
| Growth protocol |
Wild type Col-0 (CS6673) and C24 (CS22620), as well as male sterile lines that were hemizygous for a male sterility construct, were grown in 16 hours of light at 21°C and 8 hours of dark at 18°C in a controlled environment fascility. The male-sterile A. thaliana lines (ColA9 and C24A9) were pollinated by either wild type Col-0 or C24. Two biological replicates for each condition (ColA9 X C24 or C24A9 X Col-0) were used in these experiments. No emasculation was needed because all egg donors had a sterility construct.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA processing for Illumina sequencing was performed using a homemade kit (see Burkart-Waco et al. 2013 for technical details). RNA was sequenced according to Illumina's specifications on HiSeq2000 (Illumina, San Diego) (100-bp paired-end reads).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Samples 1-4 were standard RNA-seq. Samples 5-9: mRNA amplicons, PCR sequence data for validation
Seed from 3 DAP ColA9 X A. arenosa
|
| Data processing |
All sequence preprocessing was done with custom python scripts available at the Comai lab wiki (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools). Sequences were divided according to barcodes and barcodes were removed. The Illumina 1.5+ format (fastq) reads were trimmed for adaptor contamination and bases with a quality score lower than Phred 20 were also excluded using a custom python script. Reads that were shorter than 40 base pairs (for 80-bp or 100-bp). The Illumina quality scores were converted to Sanger, which is compatible with most aligners. Biological replicates were pooled for greater sequence depth.
Processed and pooled sequences were aligned to A. thaliana TAIR10 cDNA all gene models using Burrows-Wheeler Aligner (BWA) version 0.5.8c and SAM files and parsed pileups were generated using Samtools version 0.1.7 [58] as well as custom python scripts..
Read counts were generated using a custom python script available for download at http://comailab.genomecenter.ucdavis.edu/index.php/Hybrid_Transcriptome.
Genome_build: TAIR10 cDNA (all gene models)
|
| |
|
| Submission date |
Apr 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Luca Comai |
| E-mail(s) |
[email protected]
|
| Phone |
(530) 752-8485
|
| Organization name |
UC Davis
|
| Department |
Genome Center
|
| Lab |
Comai Lab
|
| Street address |
451 Health Sciences Dr
|
| City |
Davis |
| State/province |
Calif |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL16380 |
| Series (1) |
| GSE56675 |
Perturbation of parent-specific gene expression during interspecific hybridization |
|
| Relations |
| BioSample |
SAMN02725519 |
| SRA |
SRX515190 |
