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| Status |
Public on Aug 18, 2021 |
| Title |
Spodoptera frugiperda somatic samples [F93] |
| Sample type |
SRA |
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| Source name |
somatic body tissues
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| Organism |
Spodoptera frugiperda |
| Characteristics |
time point: Control
replicate: Replicate 3
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hemolymph or combination of other body tissues, which from the standpoint of bulk, consisted primarily of the fat body, epidermis, tracheal matrix and midgutody tissues (referred to as somatic body tissues) were collected and homogenized in Trizol. Samples were DNAse treated and cDNA libraries were constructed.
RNA libraries were prepared for sequencing using NEBNext Utra Directional RNA Library Prep kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
S1A.xls
S1C.xls
S1I.xls
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| Data processing |
Low sequencing quality and adapter sequences were removed from the libraries using trimmomatic-0.32
ribosomal contaminants were removed with SortMeRNA version 2.0
Sequencing reads were mapped to one or several of the following reference genome assemblies: 1) viral genome of SfAV , 2) viral genome of TnAV , 3) Spodoptera frugiperda genome, SF_CORN_1 assembly (NCBI accession GCA_900240015.1), and bowtie2 and the splice-aware program hisat2 was used for all other genomes.
Library statistics, read counts and RPKMs calculation were determined using the bedtools intersectBed program in conjunction with custom written Perl scripts (available upon request).
Genome_build: GCA_900240015.1 and ASM360422v1
Supplementary_files_format_and_content: RPKM expression levels, .xlsx files
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| Submission date |
May 11, 2021 |
| Last update date |
Aug 18, 2021 |
| Contact name |
Peter Arensburger |
| E-mail(s) |
arensburger@gmail.com
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| Organization name |
California State Polytechnic University Pomona
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| Department |
Dept. of Biology
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| Street address |
3801 Watkins Avenue
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| City |
Pomona |
| State/province |
CA |
| ZIP/Postal code |
91768 |
| Country |
USA |
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| Platform ID |
GPL27985 |
| Series (1) |
| GSE174236 |
Ascoviruses radically optimize virion proliferation by fully cleaving host cells into viral vesicles that circulate in hemolymph |
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| Relations |
| BioSample |
SAMN19107187 |
| SRA |
SRX10842235 |
| 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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