|
| Status |
Public on Nov 11, 2011 |
| Title |
4X4_seed_DAP6_small_RNA_seq |
| Sample type |
SRA |
| |
|
| Source name |
DAP6 seeds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
cross: 4x X 4x
tissue: dissected seeds
Stage: 6 Days After Pollination
|
| Treatment protocol |
Reciprocal interploidy crosses were made by pollinating diploid flowers with tetraploid pollens (2x4) or tetraploid flowers with diploid pollens (4x2) 24h after manual emasculation. Diploid and tetraploid flowers were manually self-pollinated to serve as balanced dosage controls. Seeds were dissected from the siliques at 3, 4, 5, 6, 7 days after pollination (DAP) to eliminate maternal tissue contamination. Small RNA library construction and gene expression assays were performed using the seeds dissected at 6DAP.
|
| Growth protocol |
Diploids (2n = 2x = 10) and tetraploids (2n = 4x = 20) of Arabidopsis thaliana Col-0 ecotype was grown under 16h light at 22°C and 8h darkness at 20°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from seeds and leaves using Plant RNA reagent (Invitrogen) and subjected to electrophoresis in a 15% urea-polyacrylamide gel. The small RNA fraction (18-30-nt) was recovered from the gel. The small RNAs were ligated to 5’ and 3’ RNA oligo adapters (Supplementary Table x3) and reverse-transcribed to produce first strand cDNAs, which were amplified by PCR and sequenced by Illumina Genome Analyzer II (at UC Davis Genome Center).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
balanced cross
small RNA sequencing
|
| Data processing |
Short reads (40-nt) were parsed to remove 3’ adaptors and mapped to Arabidopsis thaliana genome (TAIR9) using CASHX (http://asrp.cgrb.oregonstate.edu/db/download.html). To reduce ambiguity, only the perfectly matched reads were used for further analysis. The sequences from chloroplast and mitochondrial and structural non-coding RNAs including ribosomal RNAs, transfer RNAs, snoRNAs and snRNAs were excluded from the analysis.
|
| |
|
| Submission date |
Nov 11, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Z Jeffrey Jeffrey Chen |
| E-mail(s) |
zjchen@austin.utexas.edu
|
| 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 |
GPL9302 |
| Series (1) |
| GSE25280 |
Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds. |
|
| Relations |
| SRA |
SRX031196 |
| BioSample |
SAMN00120357 |
