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Sample GSM5777312 Query DataSets for GSM5777312
Status Public on Apr 25, 2023
Title ATH1050
Sample type SRA
 
Source name two-week-old seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype/variation: Col-0
rep: rep2
Growth protocol Seedlings grown on 1X MS, 1% (w/v) sucrose, 1% (w/v) agar for two-weeks in a climate-controlled growth chamber (21C; 16h day: 8h night); Fully expanded rosette leaves were collected from adult plants grown in soil under long day growth chamber conditions at 21/22C
Extracted molecule polyA RNA
Extraction protocol PARE libraries were prepared as per Nagarajan et al., (2019); GMUCT libraries were prepared according to Wilmann et al., 2014 with modifications suggested in Carpentier et al., 2021; RNA-seq libraries: 50 ug polyA+ RNA (2x enriched) prepared as per NEBNext Ultra II Directional Library Preparation kit;
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Description RNA-seq
gene_exp.diff
Data processing PARE libraries (Illumina HiSeq 2500); GMUCT and RNA-seq libraries (Illumina NextSeq 550)
Reads were mapped to Arabidopsis TAIR10 genome using Tophat v2.0
PARE and GMUCT libraries were analyzed as per Hurtig et al., 2021 (PNAS) using the ComPARE pipeline
Bedgraph files contain ComPARE scores from PARE and GMUCT libraries comparing normalized abundances (expressed as counts per million, CPM) at every 5'P site between Col-0, xrn4 and mfl1xrn4
Genome_build: Arabidopsis TAIR10 (Ensemble v49)
Supplementary_files_format_and_content: RNA-seq: gene_exp.diff is a cuffdiff output file; PARE and GMUCT: Genomic coordinate file (with annotations) containing RNA Degradome scores where 5'P site CPM >= 1 in xrn4 in both replicates (bedgraph files)
 
Submission date Jan 07, 2022
Last update date Apr 25, 2023
Contact name Pamela J Green
E-mail(s) green@dbi.udel.edu
Organization name Delaware Biotechnology Institute
Department Plant and Soil Sciences
Street address 15 Innovation Way
City Newark
State/province DE
ZIP/Postal code 19711
Country USA
 
Platform ID GPL24270
Series (1)
GSE193247 RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis
Relations
BioSample SAMN24724713
SRA SRX13658010

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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