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Sample GSM2328656 Query DataSets for GSM2328656
Status Public on Jan 25, 2017
Title AGO10OE-W1
Sample type SRA
 
Source name 13-day-old seedlings, without AGO1-IP
Organism Arabidopsis thaliana
Characteristics line: W1
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-5
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 Xuemei Chen
E-mail(s) xuemei.chen@ucr.edu
Organization name University of California, Riverside
Department Botany and Plant Sciences
Lab Genomics Building 4237
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 SAMN05824334
SRA SRX2191355

Supplementary file Size Download File type/resource
GSM2328656_AGO10OE-W1.tag.txt.gz 23.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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