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| Status |
Public on Jul 27, 2021 |
| Title |
PBS5_WT |
| Sample type |
SRA |
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| Source name |
Gastrocnemius_PBS
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
treatment: Phosphate buffered saline
tissue: skeletal muscle
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| Treatment protocol |
In vivo studies in ammonia-treated or vehicle-treated mice were performed in 8–10-week-old wild type animals bred on a C57BL/6J background (Jackson Laboratory, Bar Harbor, ME). In brief, an Alzet miniosmotic pump (Model 2004, Alzet, Cupertino, CA, USA) pre-filled either with ammonium acetate (Am) (released at a rate of 2.5 mmol/kg/day) or sterile phosphate buffered saline (PBS) was implanted in the mice as described previously. Mice were sacrificed 4 weeks after pump implantation and gastrocnemius muscle was rapidly collected and flash frozen.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus minikit (Qiagen, Germantown, MD)
RNAseq libraries were generated using the RNeasy Plus minikit (Qiagen, Germantown, MD) and sequenced on an Illumina HiSEQ400 instrument (using protocols provided by manufacturer) by Novogene (Sacramento, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Downstream analysis of RNAseq datasets was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene’s wrapped scripts.
Alignments were parsed using TopHat and differential expressions were determined through DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with FPKM for each sample and differential expression of genes
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| Submission date |
Apr 07, 2021 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Srinivasan Dasarathy |
| E-mail(s) |
dasaras@ccf.org
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| Phone |
216-318-7010
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| Organization name |
Cleveland Clinic Lerner Research Institute
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| Department |
Inflammation and Immunity
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| Lab |
Dasarathy Lab
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| Street address |
9500 Euclid Ave
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| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44195 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE171644 |
Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia [mouse RNA-seq] |
| GSE171645 |
Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia |
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| Relations |
| BioSample |
SAMN18648923 |
| SRA |
SRX10532497 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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