|
| Status |
Public on Jul 01, 2013 |
| Title |
rack1_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Col-0
genotype/variation: rack1abc mutant
developmental stage: 10 day-old seedlings
growth conditions: half-strength MS medium for 10 days
|
| Treatment protocol |
no special treat was applied
|
| Growth protocol |
Plants were grown on half-strength MS medium for 10 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
small RNA libraries were generated with GATC (Konstanz, Germany). Library construction was performed according to the TruSeq Small RNA Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
rack1abc small RNAs, replicate 1
|
| Data processing |
adaptor trimming (sRNA Toolkit tool=adaptor, minsize=17, maxsize=27)
mapping to TAIR10 (genomemapper, mismatches=0)
read annotation according to TAIR10 (custom perl script)
filtering for rRNA/tRNA (custom perl script)
mapping to known mature miRNA sequences (custom perl script)
differential expression analysis (edgeR, library size = total #reads after filtering for tRNA/sRNA (s.a))
Genome_build: TAIR10
Supplementary_files_format_and_content: fasta, trimmed and filtered reads
|
| |
|
| Submission date |
Sep 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sascha Laubinger |
| E-mail(s) |
sascha.Laubinger@uol.de
|
| Organization name |
University of Oldenburg
|
| Street address |
Carl-von-Ossietzky-Str. 9-11
|
| City |
Oldenburg |
| ZIP/Postal code |
D-26111 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE40579 |
RACK1 function in the miRNA pathway |
|
| Relations |
| SRA |
SRX182608 |
| BioSample |
SAMN01161875 |
