|
| Status |
Public on Nov 10, 2023 |
| Title |
LK4804-19 |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6N mouse heart tissue, WT, isoproterenol treatment
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
diet: NIH-31
tissue: Heart
genotype: WT
treatment (2_weeks): Vehicle (PBS, Sodium ascorbate, isoproterenol)
|
| Treatment protocol |
WT and OGFOD1-KO mice aged 3-5 months were treated with either vehicle (1X PBS and Sodium Ascorbate) or isoproterenol (1X PBS, Sodium Ascorbate, and Isoproterenol) for 2 weeks by osmotic minipump. Hearts were isolated from these mice and RNA was extracted and subjected to RNAsequencing.
|
| Growth protocol |
Mice were fed a standard NIH-31 diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were excised from mice, weighed, and flash-frozen using liquid nitrogen-chilled clamps. Frozen hearts were ground in to a fine powder in a chilled mortar and pestle. A small aliquot of heart powder was then used to extract RNA using Qiagen's RNeasy RNA extraction kit. Isolated RNA was stored at -80 until ready for sequencing analysis.
The library was constructed using Illumina's Truseq stranded total RNA library prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SP 300 cycle kit
LK4804-19
|
| Data processing |
Libraries were sequenced using paired-end 150-bp reads on an Illumina Novaseq 6000.
The FASTQ sequence reads were aligned to the mouse genome GRC m38 using HISAT2 v2.1.0.
Mapped reads were quantified with FeatureCounts v1.6.3 (gencode.vM23.annotation.gtf).
Gene expression analysis was completed in R version 3.6.0 using the limma 3.40.6 package.
Assembly: GRCm38/M23
Supplementary files format and content: raw_counts_gene_based_featureCounts.csv contains raw counts
|
| |
|
| Submission date |
Nov 10, 2022 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Sonja Best |
| E-mail(s) |
sbest@niaid.nih.gov
|
| Phone |
406-375-9694
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Allergy and Infectious Diseases
|
| Lab |
Laboratory of Neurological Infections and Immunity
|
| Street address |
903 South 4th Street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE217755 |
OGFOD1 Regulates Translation to Alter Hypertrophy Susceptibility |
|
| Relations |
| BioSample |
SAMN31684566 |
| SRA |
SRX18233731 |
