|
| Status |
Public on Jan 25, 2017 |
| Title |
AGO10OE-M2 |
| Sample type |
SRA |
| |
|
| Source name |
13-day-old seedlings, without AGO1-IP
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
line: M2
genotype/variation: AGO10 overexpression
age: 13 days old
developmental stage: seedling
|
| Treatment protocol |
Anti-AGO1 antibody (Agrisera) was used to immunoprecipitate AGO1-RISC
|
| Growth protocol |
13-day-old seedlings grown on ½ Murashige and Skoog (MS) plates under 16h light/8h dark cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with TRIzol reagent (Life Technologies, USA, 15596018)
For samples without AGO1-IP, small RNA fragments (~15–30 nucleotides) were selected and recovered from 10 µg of total RNAs by 15% urea-polyacrylamide gel electrophoresis. RNAs isolated from AGO1-IP RISC were used directly for making libraries without size selection. Libraries were made using the NEBNext Small RNA Library Prep kit (NEB, USA) according to manufacturer’s instructions. Briefly, 3' and 5' adapters were ligated sequentially to the small RNAs. Ligated small RNAs were converted to cDNA by reverse transcription followed by PCR amplification for 15 cycles. The barcoded libraries were sequenced on the Illumina NextSeq500.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Col-AGO10OE-4
|
| Data processing |
Raw reads were processed by first trimming 3’ adapter sequence using custom Perl script. Reads without 3’ adapter sequence or less than 18 nucleotides after trimming were discarded from further analysis.
Trimmed reads were aligned against a custom database containing rRNA, tRNA, snoRNA, and snRNAs using Bowtie 0.12.8 to filter out rRNA reads.
Trimmed reads were collapsed into unique sequences with counts (tag count files) and processed as described in Zhao et al. Curr Biol 2012 for determining 3' end truncation and tailing.
Genome_build: TAIR10
Supplementary_files_format_and_content: tag count files contain raw reads (after adapter-trimming) collapsed into unique sequences with the corresponding read count in the library. This file is used to analyze the modifications of miRNA 3'ends as described in Zhao et al. Curr Biol 2012.
|
| |
|
| Submission date |
Sep 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Meera Nair |
| E-mail(s) |
meera.nair@ucr.edu
|
| Phone |
951-827-7734
|
| Organization name |
University of California, Riverside
|
| Department |
Biomedical Sciences
|
| Lab |
3135 Multidisciplinary Building
|
| Street address |
3401 Watkins Drive
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE87348 |
ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis [AGO10OE] |
| GSE87355 |
ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis |
|
| Relations |
| BioSample |
SAMN05824335 |
| SRA |
SRX2191354 |
