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Sample GSM4625090 Query DataSets for GSM4625090
Status Public on Jun 18, 2020
Title Indoxyl-Sulphate-2
Sample type SRA
 
Source name 3T3_Indoxyl-Sulphate
Organism Mus musculus
Characteristics cell line: 3T3 cells
indoxyl sulphate treatment: 100μM
oxidative ldl treatment: None
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 Indoxyl-Sulphate-2_S12
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 SAMN15311018
SRA SRX8571439

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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