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| Status |
Public on Apr 03, 2018 |
| Title |
Nectary line 467 replicate 3 |
| Sample type |
SRA |
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| Source name |
Nectary line 467
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| Organism |
Helianthus annuus |
| Characteristics |
line: line 467
nectar production: high
tissue: Nectary tissue
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Nec467 S3 UQN
sun_nectary_467_3_S21
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| 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
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| Submission date |
Apr 01, 2018 |
| Last update date |
Apr 03, 2018 |
| Contact name |
Marshall Hampton |
| Organization name |
University of Minnesota Duluth
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| Street address |
1117 University Drive
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| City |
Duluth |
| State/province |
MN |
| ZIP/Postal code |
55812 |
| Country |
USA |
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| Platform ID |
GPL24801 |
| Series (1) |
| GSE112583 |
Transcriptome of sunflower (Helianthus annuus) nectaries and leaf |
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| Relations |
| BioSample |
SAMN08828748 |
| SRA |
SRX3871382 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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