 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 18, 2020 |
| Title |
Ox-LDL-2 |
| Sample type |
SRA |
| |
|
| Source name |
3T3_Ox-LDL
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3 cells
indoxyl sulphate treatment: None
oxidative ldl treatment: 50μg/mL
pnaktide treatment: None
|
| Treatment protocol |
3T3-L1 cells were treated with IS (100μM) or oxLDL (50μg/mL) with or without pNaKtide (0.7μM), for five days
|
| Growth protocol |
Frozen mouse pre-adipocytes (3T3-L1) were purchased from ATCC (ATCC, Manassas, VA, USA) and re-suspended in Dulbecco’s Modified Eagle Media (DMEM). 3T3-L1 cells were then supplemented with 10% heat-inactivated fetal bovine serum and 1% antibiotic/antimycotic solution. The cells were plated at a density of 1–5 x 106 cells per 25 cm2 dish. The cultures were maintained at 37οC in a 5% CO2 incubator and the medium was changed after 48 h and every 3–4 days thereafter. When the 3T3-L1 cells were confluent, the cells were recovered by the addition of trypsin. The 3T3-L1 cells (Passage 2–3) were plated in a 6- and 24-well plates at a density of 10,000 cells/cm2 and cultured in DMEM to achieve at least 80% confluency. The medium was replaced with adipogenic medium and the cells were cultured for an additional five days. The adipogenic media consisted of complete culture medium supplemented with DMEM-high glucose, 10% (v/v) FBS, 10 _g/mL insulin, 0.5 mM dexamethasone (Sigma-Aldrich, St. Louis, MO, USA), 0.5 mM isobutylmethylxanthine (Sigma-Aldrich, St. Louis, MO, USA) and 0.1 mM indomethacin (Sigma-Aldrich, St. Louis, MO, USA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from adipose tissue using RNeasy Protect Mini Kit (QIAGEN, Maryland)
Libraries were prepared from 1 ug total RNA per sample using the Truseq strand mRNA kit (Illumina , San Diego, CA) according to the manufacturers’ instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Ox-LDL-2_S22
|
| Data processing |
Reads were trimmed to remove adapters and low-quality base calls using Trimmomatic v0.38
Reads were aligned to the reference genome GRCm38 using HISAT2 v2.1.0
Count tables were generated using GenomicAlignments v1.16.0
Data were analyzed using DESeq2 v1.20.0. Raw and normalized count tables, and FPKM values as computed by DESeq2, were exported as CSV files
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_counts.csv: raw read counts per gene per sample
Supplementary_files_format_and_content: normalized_counts.csv: read counts per gene per sample, normalized by library size by DESeq2
Supplementary_files_format_and_content: fpkm.csv: FPKM values per gene per samples as computed by the DESeq2 function fpkm()
|
| |
|
| Submission date |
Jun 17, 2020 |
| Last update date |
Jun 19, 2020 |
| Contact name |
James Denvir |
| E-mail(s) |
denvir@marshall.edu
|
| Organization name |
Marshall University School of Medicine
|
| Department |
Biochemistry and Microbiology
|
| Lab |
Genomics and Bioinformatics Core Facility
|
| Street address |
One John Marshall Drive
|
| City |
Huntington |
| State/province |
WV |
| ZIP/Postal code |
25755 |
| Country |
USA |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE152724 |
Expression profiling by RNA-Seq of 3T3 mouse pre-adipocyte cells after treatment with Indoxyl Sulphate or Oxidative LDL, with or without pNaKtide |
| GSE152725 |
Oxidant Alterations in Adipocyte mRNA Expression: Role of the Na,K-ATPase Oxidant Amplification Loop |
|
| Relations |
| BioSample |
SAMN15311008 |
| SRA |
SRX8571449 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
