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Status |
Public on Feb 20, 2022 |
Title |
Uninfested control, rep 2 [C2_S50] |
Sample type |
SRA |
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Source name |
leaf tissue
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Organism |
Solanum lycopersicum |
Characteristics |
tissue: leaf variety: Moneymaker age: 9 weeks treatment: Uninfested control
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Extracted molecule |
total RNA |
Extraction protocol |
Plant RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s protocol RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
cDNA libraries were developed using the TruSeq RNA Library Prep Kit v2 following the manufacturer's protocol Libraries were multiplexed and sequenced on the Illumina PE HiSeq 2500 v4 platform Sequence cluster identification, quality prefiltering, base calling, and uncertainty assessment were done in real time using Illumina’s HCS 2.2.38 and RTA 1.18.61 software with default parameter settings bioinformatic analysis was performed using the HISAT2-StringTie-Ballgown RNA-Seq workflow Genome_build: Libraries reads were mapped to the S. lycopersicum genome (vSL3.0) using HISAT2; StringTie assembled hits to known transcripts based on the vITAG3.2 annotation Supplementary_files_format_and_content: Matrix table with fpkm (Fragments Per Kilobase of transcript per Million mapped reads) values for every gene and every sample
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Submission date |
Feb 17, 2022 |
Last update date |
May 10, 2022 |
Contact name |
Kyle Harrison |
E-mail(s) |
kyle.harrison@usda.gov
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Organization name |
Texas A&M University
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Department |
Entomology
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Street address |
2475 TAMU
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City |
College Station |
ZIP/Postal code |
77843 |
Country |
USA |
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Platform ID |
GPL19694 |
Series (1) |
GSE196951 |
Effects of ‘Candidatus Liberibacter solanacearum’ haplotypes A and B on tomato gene expression and geotropism |
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Relations |
BioSample |
SAMN26026202 |
SRA |
SRX14211880 |
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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