|
| Status |
Public on Jul 30, 2021 |
| Title |
48hpi-rep2-H |
| Sample type |
SRA |
| |
|
| Source name |
TnAV 48h infected Trichoplusia ni caterpillar (Hemolymph)
|
| Organism |
Trichoplusia ni |
| Characteristics |
virus name/genotype: Trichoplusia ni ascovirus-6a1 variant
tissue: Hemolymph
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected from healthey or TnAV-6a1 variant infected (third or early fourth instars) Trichoplusia ni larval hemolymph or fat body, epidermis and tracheal matrix tissues using TRIzol (Invitrogen), followed by using 5 ug total RNA as the starting material for DNase-treatment by RNA Clean and Concentrator TM-5 kit (ZYMO RESEARCH).
After the DNase-treatment of total RNA, the mRNA was isolated from each sample using the NEB NextPoly(A) mRNA magnetic isolation module kit (New England Biolabs). The cDNA libraries were then prepared following the manufacturer's instructions of NEBNext® Ultra™ Directional RNA Library Prep Kit (New England Biolabs) for Illumina®. For each time point in the two tissues under study we sequenced two biological replicates.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina adapter sequences were removed and low quality sequencing reads removed using Trimmomatic software
Ribosomal contaminant sequences were removed using sortMeRNA software
Reads were aligned to reference genome using Bowtie2 software
Transcript expression was estimated using custom written Perl scripts and reported as log base2 transformed RPKMs
Reads assembled into contig using Trinity software, contigs were oriented and further assembled using CAR software
Supplementary_files_format_and_content: Transcript expression values are reported as log2 transformed RPKM values in Microsoft Excel spreadsheet format, contig assembly sequences are reported as a plain text file
|
| |
|
| Submission date |
May 24, 2018 |
| Last update date |
Jul 30, 2021 |
| Contact name |
Heba A. H. M. Zaghloul |
| E-mail(s) |
[email protected]
|
| Phone |
9518275710
|
| Organization name |
University of California, Riverside
|
| Department |
Entomology
|
| Lab |
Dr. Brian Federici's lab
|
| Street address |
900 University Ave
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL23793 |
| Series (1) |
| GSE114902 |
Expression patterns of TnAV-6a1 genes in the combination of fat body, Epidermis and tracheal matrix tissues compared to hemolymph viral vesicles. |
|
| Relations |
| BioSample |
SAMN09258290 |
| SRA |
SRX4123132 |
