|
| Status |
Public on Mar 18, 2014 |
| Title |
ddm1-2 [PARE-seq] |
| Sample type |
SRA |
| |
|
| Source name |
mix-stage inflorescence
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: mix-stage inflorescence
genotype/variation: ddm1-2
|
| Growth protocol |
Arabidopsis grown under standard long day growth conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mix-stage inflorescence (contain majority of unopened flower buds) were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Invitrogen) according to manufacturer's protocol.
PARE: Degradome libraries (PARE) libraries were constructed as previously described (Zhai et al. 2013 PMID: 23810899). The libraries were sequenced on an Illumina HiSeq at the Delaware Biotechnology Institute (Newark, DE).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Degradome analysis in Arabidopsis to validate microRNA prediction cleavage sites at transposons.
|
| Data processing |
The adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides.
Genome_build: Arabidopsis TAIR10 genome
Supplementary_files_format_and_content: tag count file
|
| |
|
| Submission date |
Nov 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kate M Creasey |
| Organization name |
Cold Spring Harbor Laboratory
|
| Department |
Plant Sciences
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE52342 |
miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis [PARE-seq] |
| GSE52952 |
miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis |
|
| Relations |
| BioSample |
SAMN02422676 |
| SRA |
SRX384363 |
