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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 08, 2024 |
| Title |
Mammary epithelial tumor-derived cells from wild-type NIC mice with conditional Cpt1a alleles_1B [WT_5257B_biol rep 2] |
| Sample type |
SRA |
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| Source name |
Mammary epithelium
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| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary epithelium
cell line: Primary mammary epithelial cells
cell type: Primary mammary epithelial cells
genotype: NIC/wild-type
treatment: None
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| Treatment protocol |
No treatments were applied to the biological material prior to extraction.
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| Growth protocol |
Mammary tumors at 8 weeks post-palpation were excised from female MMTV-NIC and MMTV-NIC/Cpt1a flx flx mice, dissociated and plated in Complete Media, consisting of DMEM (Wisent, 319-005-CL) supplemented with 2% FBS (Wisent, 080-150), 5ng/ml EGF (Winsent, 511-110-UM) 1 μg/ml Hydrocortisone (Sigma, H4001), 5 μg/ml Insulin (Wisent, 511-016-UG), 35 μg/ml Bovine Pituitary Extract (BPE – Hammond CellTech, 1078-NZ) and 50 ug/ml Penicillin/Streptomycin (Wisent, 450-200-EL). Cells were maintained in a humidified, 5% CO2, 37 degrees C incubator in Complete Media. Cells were authenticated by PCR-based genotyping (oligonucleotide details in Supplementary Table S1) and by immunoblotting to detect Cpt1a expression. All cell lines were tested biweekly for mycoplasma using the MycoAlert Kit (Lonza, LT07-118). All cells used in this study were negative for mycoplasma contamination.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNEasy Mini kit was used according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Library Prep Kit following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Processed data file column Q
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| Data processing |
Adaptor sequences and low quality score bases (Phred score < 30) were trimmed using Trimmomatic (Bolger et al., 2014)
Reads were aligned to the GRCm38 mouse reference genome assembly using STAR (Dobin et al., 2012)
Read counts were obtained using HTSeq (Anders et al., 2015) with parameters -m intersection-nonempty -stranded=no
Raw counts were normalized using edgeR’s TMM algorithm (Robinson et al., 2010) and were then transformed to log2-counts per million (logCPM) using the voom function implemented in the limma R package (Ritchie et al., 2015)
To assess differences in gene expression levels between the different conditions, we fitted a linear model using limma’slmfit function(method="robust" parameter was applied for end-stage tumor dataset)
Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method
Assembly: Distinct patterns of gene expression changes were identified using unsupervised hierarchical clustering method (R function hclust with Euclidean distance and complete linkage metrics)
Supplementary files format and content: GrCM38/mm10
Supplementary files format and content: A tab-delimited text files includes RPKM values for all samples.
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| Submission date |
Jan 30, 2024 |
| Last update date |
Jul 08, 2024 |
| Contact name |
Sherif Samer Attalla |
| E-mail(s) |
sherif.attalla@mail.mcgill.ca
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| Organization name |
McGill
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| Department |
Goodman Cancer Institute
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| Lab |
Muller lab
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| Street address |
1160 Ave. Pine W
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3A1A3 |
| Country |
Canada |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE254622 |
Targeting Fatty Acid Oxidation Enhances Response to HER2-targeted Therapy |
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| Relations |
| BioSample |
SAMN39676848 |
| SRA |
SRX23454228 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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