|
| Status |
Public on Nov 17, 2024 |
| Title |
Female pubertal n-3 polyunsaturated fatty acid mammary epitheial cells, TG2 |
| Sample type |
SRA |
| |
|
| Source name |
inguinal mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
Sex: Female
age: Puberty (6-8 weeks)
tissue: inguinal mammary gland
cell type: pooled mammary epitheial cell
genotype: Transgenic fat-1 (FVB/NJ)
diet: Modified AIN93G diet (Research Diets Inc.), 22% kcal from fat, 10% fat (w/w) from safflower oil
time of_dietary_exposure: Maintained on Parental Diet (lifelong)
|
| Treatment protocol |
Mammary epithelial cells were isolated using the Prater method. In brief, finely minced mammary glands were digested in collagenase/hyaluronidase (StemCell, cat # 07912) for 18 h at 37◦C to allow for tissue dissociation. Cells were washed in Hank’s balanced salt solution (Sigma, cat # H6648) and treated with ammonium chloride (Sigma, cat # A9434), Trypsin/EDTA (Sigma, cat # T4049), dispase (StemCell, cat # 07913) and DNAase 1 (Sigma, cat # D5025) to release the epithelial cells. Five million cells were used for total RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Purelink RNA Mini Kit (Thermo Fisher Scientific, cat # 12183018A) following the kit instructions. The purity of the RNA was assessed using the Agilent bioanalyzer 2100 where all samples had a RNA integrity number (RIN) greater than 9 (out of a 10 point scale). RNA samples were stored at -80 ℃ for later analysis.
mRNA library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
The fat-1 transgene from the roundworm Caenorhabditis elegans encodes for n-3 desaturase, enabling endogenous whole-body production of n-3 PUFA from n-6 PUFA (safflower oil), including the mammary gland
TG2
|
| Data processing |
The pilot dataset was analyzed following the protocol from Pertea et al (the ``new Tuxedo” package)
The reads from the samples were mapped to the reference genome GRCM38 using HISAT2
All six samples had an overall alignment rate greater than 97%.
The alignments were then passed to String Tie for transcript assembly and quantification.
The transcript abundance matrix from String Tie was then used for differential expression analysis using two different approaches: edgeR and DESeq2.
Assembly: GRCM38 using HISAT2
Supplementary files format and content: text file countains raw gene counts for each sample
|
| |
|
| Submission date |
Nov 14, 2024 |
| Last update date |
Nov 17, 2024 |
| Contact name |
Connor D.C Buchanan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Guelph
|
| Department |
Human Health and Nutritional Sciences
|
| Lab |
David Ma ([email protected])
|
| Street address |
50 Stone Road East
|
| City |
Guelph |
| State/province |
Ontario |
| ZIP/Postal code |
N1G2W1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE281867 |
RNA-Seq analysis of pubertal mammary epithelial cells reveals novel n-3 polyunsaturated fatty acid transcriptomic changes in the fat-1 mouse model |
|
| Relations |
| BioSample |
SAMN44739489 |
| SRA |
SRX26725122 |
