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| Status |
Public on Dec 05, 2023 |
| Title |
DON-Treated1 |
| Sample type |
SRA |
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| Source name |
Mammary gland
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| Organism |
Bos taurus |
| Characteristics |
tissue: Mammary gland
cell line: MAC-T
cell type: Mammary epithelial cells
genotype: WT
treatment: DON
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| Treatment protocol |
The bovine macrophage (BoMac) cell line was cultured in a T25 culture flask (Corning, Tewksbury, MA, USA) using Roswell Park Memorial Institute 1640 medium (RPMI 1640; Invitrogen, Burlington, ON, Canada). The culture medium was supplemented with 2.0 mM L-glutamine, 10% heat-inactivated fetal bovine serum (FBS; Invitrogen), 2.5 mM HEPES buffer (Invitrogen), 1 mM Sodium Pyruvate (Invitrogen), and 1% Antibiotic-Antimycotic (containing 100 units/mL of penicillin, 100 µg/mL of streptomycin, and 0.25 µg/mL of amphotericin B; Invitrogen). The cells were maintained at 37 °C in an atmosphere containing 5% CO2.
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| Growth protocol |
The bovine epithelial cell line (MAC-T) was cultured in a T25 culture flask (Corning, Tewksbury, MA, USA) according to the previous protocol in Dulbecco’s modified Eagle medium (DMEM), supplemented with 10% fetal bovine serum and penicillin/streptomycin (100 U/mL; Invitrogen, Waltham, MA, USA; Thermo Fisher Scientific, Inc., Waltham, MA, USA), and maintained in an incubator at 37 °C with 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the MAC-T cells of the co-culture system 48 h after mycotoxin exposure using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Illumina Seq library preparation kit using the manufacturer instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample 7
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| Data processing |
CLC genomics workbench
Sequence reads were trimmed for adaptor sequences using CLC genomics workbench.
Trimmed sequences were mapped to Bovine genome Bos_Taurus.ARS-UCD1.2.101 using CLC genomics workbench
Read count extraction and normalization were performed using CLC genomics benchwork
Assembly: Bos_Taurus.ARS-UCD1.2.101
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM for each sample
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| Submission date |
Nov 30, 2023 |
| Last update date |
Dec 05, 2023 |
| Contact name |
Umesh K. Shandilya |
| E-mail(s) |
ushand@uoguelph.ca
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| Organization name |
University of Guelph
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| Department |
Animal Biosciences
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| Street address |
50 Stone Rd E
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| City |
Guelph |
| State/province |
Ontario |
| ZIP/Postal code |
N1G2W1 |
| Country |
Canada |
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| Platform ID |
GPL19172 |
| Series (1) |
| GSE249060 |
Evaluation of Immunomodulatory Effects ofFusariumMycotoxins Using Bacterial Endotoxin-Stimulated Bovine Epithelial Cells and Macrophages in Co-Culture |
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| Relations |
| BioSample |
SAMN38526199 |
| SRA |
SRX22700800 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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