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Sample GSM2258433 Query DataSets for GSM2258433
Status Public on Jul 21, 2017
Title 407179T2CF Rep 3
Sample type SRA
 
Source name leaf tissue, second trifoliate, sensitive, charcoal filtered
Organism Glycine soja
Characteristics genotype: 407179
tissue: leaf
leaf position: Second trifoliate
treatment: Charcoal filtered
Treatment protocol Plants were exposed to a 75 ppb ozone treatment for 7 hours alongside a charcoal-filtered control at < 10 ppb ozone.
Growth protocol Plants were germinated in a charcoal-filtered greenhouse and moved to continuously stirred tank reactors (CSTRs) at 2 weeks in Raleigh, NC.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Qiagen Plant RNeasy Mini Kit (Cat No./ID: 74904) with on-column DNase I digest.
Standard Illumina Protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Processed data file: gene_exp.diff
Data processing Fast-X Toolkit was used to trim off adapters and remove low-quality reads (PHRED <= 33).
Aligned to soybean reference genome and supplied annotations Gmax_275_Wm82.a2.v1 using TopHat 2.0.13.
Transcript Assembly completed using Cufflinks 2.2.1.
Differential expression tested using cuffdiff 2.2.1 with parameters --max-bundle-frags 500000 -b -u
Genome_build: Gmax_275_Wm82.a2.v1
Supplementary_files_format_and_content: gene_exp.diff: Tab-delimited differential expression file using FPKM values.
 
Submission date Aug 03, 2016
Last update date Jul 26, 2022
Contact name Nathan Waldeck
E-mail(s) nathanwaldeck2022@u.northwestern.edu
Organization name Northwestern University
Street address 303 E Superior St, Lurie 7-220
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
 
Platform ID GPL22279
Series (1)
GSE85146 RNA-Seq Study Reveals Genetic Responses of Diverse Wild Soybean Accessions to Increased Ozone Levels
Relations
BioSample SAMN05509113
SRA SRX1997414

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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