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Sample GSM3073238 Query DataSets for GSM3073238
Status Public on Apr 03, 2018
Title Nectary line 441 replicate 2
Sample type SRA
 
Source name Nectary line 441
Organism Helianthus annuus
Characteristics line: line 441
nectar production: low
tissue: Nectary tissue
Extracted molecule total RNA
Extraction protocol RNA was extracted from nectaries by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for barcoded library creation and Illumina HiSeq 2500 sequencing. Twenty-four TruSeq RNA v2 libraries were created (triplicate samples for nectaries from seven lines and triplicate leaf samples from one line) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two lanes to achieve the equivalent of approximately one lane of output. This generated 330 M reads and the average quality scores were above Q30.
Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Nec441 S2 UQN
sun_nectary_441_2_S11
Data processing Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn
Contigs mapped to closest Arabidopsis thaliana and Uniref50 references
genome_build: Uniref50 data downloaded from Uniprot:
ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/
A. thaliana reference Araport 11, release 201606:
https://www.araport.org/downloads/Araport11_Release_201606
Supplementary_files_format_and_content: Excel file of normalized counts mapped to assembled contigs, with averages and standard deviations; contigs annotated with Arabidopsis thaliana and Uniref50 closest matches
 
Submission date Apr 01, 2018
Last update date Apr 03, 2018
Contact name Marshall Hampton
Organization name University of Minnesota Duluth
Street address 1117 University Drive
City Duluth
State/province MN
ZIP/Postal code 55812
Country USA
 
Platform ID GPL24801
Series (1)
GSE112583 Transcriptome of sunflower (Helianthus annuus) nectaries and leaf
Relations
BioSample SAMN08828758
SRA SRX3871372

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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