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Sample GSM2328676 Query DataSets for GSM2328676
Status Public on Jan 25, 2017
Title AGO1IP-SDN-br2
Sample type SRA
 
Source name 13-day-old seedlings, with AGO1-IP
Organism Arabidopsis thaliana
Characteristics genotype/variation: His-FLAG-AGO10 transgenic
rip antibody: anti-AGO1 (Agrisera, AS09 527)
treatment: SDN
biological replicate: 2
age: 13 days old
developmental stage: seedling
Treatment protocol AGO1- and AGO10-RISC were immunoprecipitated (IP) from His-FLAG-AGO10 transgenic plants using anti-AGO1 (Agrisera) and anti-FLAG (Sigma) antibodies, respectively. Beads containing AGO1- or AGO10-IP were resuspended in reaction buffer (50 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT, 2.5 mM MnCl2, 1mM ATP) and then incubated with SDN1 or SDN1-D283A catalytic mutant for one hour. Beads were collected after incubation for RNA extraction.
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)
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-HFAGO10-AGO1-IP-SDN-br2
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)
GSE87351 ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis [AGO10SDN]
GSE87355 ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis
Relations
BioSample SAMN05824386
SRA SRX2191363

Supplementary file Size Download File type/resource
GSM2328676_HFAGO10.AGO1-IP-SDN.br2.tag.txt.gz 15.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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