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Sample GSM7142697

Query DataSets for GSM7142697

Status

Public on Mar 24, 2024

Title

Z. cucurbitae, 0.1x dose, 24 hpi, rep 2

Sample type

SRA

Source name

whole body fly tissue

Organism

Zeugodacus cucurbitae

Characteristics

tissue: whole body fly tissue
developmental stage: third-instar larva
time: 24 h post injection
treatment: 0.1x viral dose

Extracted molecule

polyA RNA

Extraction protocol

Each fly was collected in 300 µL TRIsure (Bioline), a guanidine thiocyanate and phenol mixture, and immediately bead homogenized prior to storage at -80℃ . Total RNA was isolated from homogenized samples using the Zymo Direct-zol-96 RNA Purification Kit performed on a KingFisher Flex instrument, which included a mid-protocol DNase I (6U/µL, 5µL) treatment, as well as a secondary Zymo DNase I treatment following RNA isolation. Final RNA was eluted in 20 µL nuclease-free water. RNA quality was assessed using a 4200 TapeStation System with RNA ScreenTape (Agilent), and 3 of the 6 replicates with highest quality for each treatment were selected to constitute the final 81 samples submitted for sequencing.
Messenger RNA library was formed by polyA capture (or rRNA removal) and reverse transcription of cDNA, performed by Novogene Corporation Inc.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_24_3

Data processing

Raw read pairs were quality filtered using Trimmomatic v0.38 with default settings, which resulted in > 99.99% read pairs retained for each sample.
Virus differential gene expression analysis was conducted on the 54 virus-infected samples by first mapping quality-filtered reads onto the DlEPV reference genome using HISAT2 v2.2.1.
StringTie v2.1.1 was used on each sample with the ‘-eB’ flag to quantify the expression for each DlEPV gene, measured in reads per kilobase per million sequenced reads (RPKMS).
Ballgown v2.26.0 was then used to perform differential expression testing of viral genes among the different fly species for each nonzero time point and dosage combination by using default settings, except the ‘libadjust’ option was set to “FALSE”
Quality-filtered read pairs from each sample were then mapped to its respective fly reference genome using HISAT2.
Fly transcript abundances were estimated with StringTie ‘-eB’ and measured in fragments per kilobase per million mapped reads (FPKM).
Assembly: Diachasmimorpha longicaudata entomopoxvirus (GenBank accession KR095315)
Assembly: Bactrocera dorsalis (Refseq accession GCF_000789215.1)
Assembly: Ceratitis capitata (Refseq accession GCF_000347755.3)
Assembly: Zeugodacus cucurbitae (Refseq accession GCF_000806345.1)
Supplementary files format and content: DlEPV_all_sample_log2_rpkms.csv: comma-delimited text file contains log2-transformed RPKMS values for each gene (rows) in each of the 81 samples (columns)
Supplementary files format and content: Bdor_all_gene_fpkm.csv: comma-delimited text file contains FPKM values for each B. dorsalis gene (rows) in each of the 27 B. dorsalis tissue samples (columns)
Supplementary files format and content: Ccap_all_gene_fpkm.csv: comma-delimited text file contains FPKM values for each C. capitata gene (rows) in each of the 27 C. capitata tissue samples (columns)
Supplementary files format and content: Zcur_all_gene_fpkm.csv: comma-delimited text file contains FPKM values for each Z. cucurbitae gene (rows) in each of the 27 Z. cucurbitae tissue samples (columns)

Submission date

Apr 04, 2023

Last update date

Mar 24, 2024

Contact name

Kelsey Coffman

E-mail(s)

kelsey.coffman@usda.gov

Organization name

USDA-ARS

Department

Tropical Pest Genetics and Molecular Biology Research Unit