|
| Status |
Public on Oct 14, 2013 |
| Title |
pap1-D/SSU_amiR21-CHS |
| Sample type |
SRA |
| |
|
| Source name |
3- week old plants grown on MSN
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
background: pap1-D
tissue-type: aerial
|
| Treatment protocol |
none
|
| Growth protocol |
16 hour light on MS media for 3 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
Library prep was per the TruSeq small RNA protocol (performed by the Australian Genome Research Facility) with an input of 3ug of RNA and 11 amplification cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Illumina (CASAVA 1.8.2)
fastx_clipper to remove barcodes
bowtie alignment
samtools (sorting, indexing, counting)
UEA sRNA toolkit phasing analysis against TAIR10 cDNA representative
Genome_build: TAIR10
Supplementary_files_format_and_content: SSU_hpCHS.csv,nd SSU_amiR21-CHS.csv and SSU_amiR21-CHS.csv contain tables describing abundance of 21-, 22- and 24-nt sRNAs in regions surrounding the the described hairpin RNA and artificial micro-RNA target sites in lines expressing the corresponding transgene. amiRNA-abundance.csv describes the abundance of a number of forms of the articial miRNA present in these samples. locuslist.csv and srnas.txt are the output of UEA sRNA toolkit phasing analysis. The data in these files is presented in supplementary material of the Plant Journal publication associated with this submission (McHale et al. 2013).
|
| |
|
| Submission date |
Aug 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Marcus McHale |
| E-mail(s) |
marcus.mchale@sydney.edu.au
|
| Organization name |
University of Sydney
|
| Department |
School of Molecular Biology
|
| Lab |
Waterhouse Lab
|
| Street address |
Lvl 8 Biochemistry Bldg G08, University of Sydney
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2006 |
| Country |
Australia |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE49792 |
Small RNA from Arabidopsis thaliana with RNA silencing directed to Chalcone Synthase (At5G13930) by a hairpin RNA, a 21-nt artificial miRNA and a 22-nt artificial miRNA in the pap1-D over-expressing background |
|
| Relations |
| BioSample |
SAMN02315631 |
| SRA |
SRX333615 |
