|
| Status |
Public on Dec 31, 2018 |
| Title |
small RNA-seq of rdr2 x wild type |
| Sample type |
SRA |
| |
|
| Source name |
whole seeds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
cross: rdr2 x wild type
tissue: whole seeds
Stage: 6 Days After Pollination
|
| Treatment protocol |
Flowers in the floral stage 12C were manually emasculated and pollinated at 24 hours after emasculation. Seeds were collected at designated days after pollination (DAP) for RNA extraction, GUS staining and functional assays. Wild-type (Col-0) seeds at the linear cotyledon stage (6 DAP) were manually dissected into embryo, endosperm and seed coat. Embryos were rinsed three times with 0.3 M Sorbitol before RNA extraction.
|
| Growth protocol |
All plants were grown under an illumination cycle of 16-h day and 8-h night at 22oC (day) and 20oC (night).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Plant RNA Reagent (Invitrogen, http://www.invitrogen.com/).
Small RNA libraries were prepared as previously described. In brief, an aliquot of 10 µg of total RNA was resolved in a 15% urea-polyacrylamide gel, and the fraction of 18-30-nt small RNAs was recovered. For nrpd1a and rdr2 mutants and their crosses, whole seeds dissected from ~20 siliques were used for each library. For manually dissected seed, the embryo, endosperm and seed coat dissected from ~50 siliques were used for each library. Purified small RNAs were ligated to 5’ and 3’ RNA oligo adapters and reverse transcribed to produce first-strand cDNAs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Small RNA sequences were trimmed for 3’ adapters, collapsed into unique sequences and mapped to A. thaliana genome (TAIR10, November 2010 release) using CASHX with perfect match option (http://carringtonlab.org/resources/cashx).
The sequences from chloroplast, mitochondrial, tRNAs, rRNAs, snoRNAs, and snRNAs were excluded from the analysis.
Small RNA reads were normalized by dividing the total number of reads of a library by 10 millions.
Multiple-hit read was assigned equally to each locus and divided by the number of hits in the genome.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample. FIELD #1: chromosome; #2: start; #3: end; #4: strand; #5: small_RNA_length; #6: normalized_read_count
|
| |
|
| Submission date |
Jun 06, 2013 |
| Last update date |
Jan 28, 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) |
| GSE47722 |
Maternal siRNAs mediate spatial and temporal regulation of gene expression and seed development in Arabidopsis |
|
| Relations |
| BioSample |
SAMN02192029 |
| SRA |
SRX297373 |
