|
| Status |
Public on Oct 15, 2022 |
| Title |
A0036, 24h, blood |
| Sample type |
SRA |
| |
|
| Source name |
Monodelphis domestica whole blood
|
| Organism |
Monodelphis domestica |
| Characteristics |
tissue: whole blood
strain: LSD
treatment: untreated
cultured time: 24h
|
| Treatment protocol |
Perfluorooctanoic acid (PFOA) and ammonium perfluoro(2-methyl-3-oxahexanoate) (GenX) were purchased from Sigma-Aldrich. (Chemical Abstracts Service Registry No. (CASRN) PFOA:335-67-1, GenX:62037-80-3). Stock solutions were prepared by dissolving neat chemical into molecular-grade dimethyl sulfoxide (DMSO) (>99.9%) at various concentrations. DMSO concentration was calculated and adjusted to achieve a final 0.1% volume percent (v/v) in all treatment and control groups. We use two final concentrations for each treatment, PFOA: 400uM/800uM, GenX: 600uM/1200uM.
|
| Growth protocol |
In the pilot experiment (Exp1), samples were diluted 1:2 and 1:4 with sterile RPMI-1640 culture medium complemented with 2 mM glutamine and antibiotics (100 U/mL penicillin and 100 μg/mL streptomycin). In the main experiment (Exp2), the blood samples were diluted 1:2 with sterile RPMI-1640 culture medium complemented with 2 mM glutamine and antibiotics (100 U/mL penicillin and 100 μg/mL streptomycin). The samples were cultured in sterile 12-well culture plates with lid (USA Scientific, FL) in CO2 incubator at 37 °C under 5 % CO2 atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA/RNA extraction were conducted using Zymo Quick-DNA/RNA Miniprep Plus Kit (Zymo Research, CA) according to the manufacturer’s instructions. DNA/RNA quantity was measured using Qubit Fluorometer 3.0 (Thermo Fisher Scientific, MA) with Qubit RNA BR Assay Kit. Samples with a good RNA quality were selected for RNA sequencing libraries.
RNA sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, MA). We checked the final concentrations and size distribution of the libraries with Qubit and LabChip GX Touch HT machine (HT DNA NGS 3K Assay) (Perkin Elmer, MA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Illumina mRNA-seq
Exp1_Sample7
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz
|
| Data processing |
FastQC (version 11.5) software was used for quality check.
Sequencing adapter sequences and low-quality bases were trimmed using Trimmomatic v0.36.
High-quality reads were mapped to the reference M.domestica genome assembly (MonDom5) by Tophat-2.1.1, Bowtie2 and star-2.7.5.
Gene counts generation were performed with Bedtools -2.30.0.
EdgeR package in R (version 4.1.2) were used to normalize and detect DEGs. The cutoff for detecting significant DEGs were |log2(fold change)| > 1 and FDR < 0.05
Assembly: M.domestica genome assembly (MonDom5) (GenBank: GCA_000002295.1)
Supplementary files format and content: Gzipped, tab-delimited text file including raw gene counts for every gene in all samples in Exp2
|
| |
|
| Submission date |
Jul 14, 2022 |
| Last update date |
Oct 15, 2022 |
| Contact name |
Xu Wang |
| E-mail(s) |
xzw0070@auburn.edu
|
| Organization name |
Auburn University
|
| Department |
Pathobiology, College of Veterinary Medicine
|
| Street address |
273 CASIC Building, Auburn Research Park, 559 Devall Dr
|
| City |
Auburn University |
| State/province |
AL |
| ZIP/Postal code |
36849 |
| Country |
USA |
| |
|
| Platform ID |
GPL30856 |
| Series (1) |
| GSE208237 |
Blood transcriptome responses to PFOA and GenX treatment in the marsupial biomedical model Monodelphis domestica |
|
| Relations |
| BioSample |
SAMN29756832 |
| SRA |
SRX16245190 |
