|
| Status |
Public on Jun 10, 2020 |
| Title |
CTR-GFP-1 |
| Sample type |
SRA |
| |
|
| Source name |
Adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
model (partial nephrectomy or sham operation): Sham
expressed protein: GFP
|
| Treatment protocol |
Mice underwent either 5/6 nephrectomy involving ligation of the left kidney leaving 1/3 functional and removal of the right kidney (PNX); or a sham operation (CTR) without ligation of the left kidney or removal of the right kidney.
Lentivirus (100µL, 2x109 TU/mL), with NaKtide or its counterpart Lenti-eGFP, driven by adiponectin promoter, was injected into the C57BL6 mice intraperitoneally (i.p.) in saline
|
| 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 |
| |
|
| 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 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
|
| |
|
| Submission date |
Jun 10, 2019 |
| Last update date |
Jun 10, 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) |
| GSE132455 |
Expression profiling by RNA-Seq of adipose tissue in mice after partial nephrectomy and administration of pNaKtide |
| GSE152725 |
Oxidant Alterations in Adipocyte mRNA Expression: Role of the Na,K-ATPase Oxidant Amplification Loop |
|
| Relations |
| BioSample |
SAMN12003091 |
| SRA |
SRX6029575 |
