|
| Status |
Public on May 07, 2021 |
| Title |
Atria_DKO_Female_F14 |
| Sample type |
SRA |
| |
|
| Source name |
heart atria
|
| Organism |
Mus musculus |
| Characteristics |
tissue: heart atria
genotype: Ipr/Ldlr DKO
gender: female
library barcode: CTTGGTAT-CCAAGTCC
|
| Treatment protocol |
Mice of both genders were fed a high salt diet (HSD, 8% NaCl, TD.92012, Harlan Teklad, Madison, WI) and saline containing 0.9% NaCl (Hospira, Lake Forest, IL) from 8-10 weeks of age for two weeks. Mice were weighed before and after the HSD feeding.
|
| Growth protocol |
Mice were housed in groups on a 12 hour light, 12 hour dark schedule. feed type : regular chow; diet availability : ad libitum; diet supplements : none; water supply type : bottle; water type : tap
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Heart atria and kidney medulla were collected from animals perfused with ice-cold PBS dissolved in UltraPure DEPC-treated water to minimize degradation of RNA. The tissues were immediately stored separately in RNAlater solution at 4ºC. After 24h, the tissue samples were transferred to -80ºC for storage until analyses. RNA was extracted using TRIzol Reagent and RNeasy Kit following the manufacturer’s protocol.
RNA integrity was checked on an Agilent Technologies 2100 Bioanalyzer. RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw RNA-seq reads were aligned to the GRCm38 build of the mouse genome by STAR v2.7.6a, with the following command line parameters: --outSAMunmapped Within KeepPairs--outFilterMismatchNmax33--seedSearchStartLmax33--alignSJoverhangMin 8. Additionally, STAR was provided with the gene models (Ensembl v91) in GTF format during alignments.
Data were normalized and quantified at both gene and exon-intron level, using a downsampling strategy implemented in the PORT pipeline (github.com/itmat/Normalization -v0.8.45e-beta).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files contain PORT-normalized/quantified gene-level read counts from uniquely-aligned reads that map to single genes.
|
| |
|
| Submission date |
May 06, 2021 |
| Last update date |
May 07, 2021 |
| Contact name |
Gregory Robert Grant |
| E-mail(s) |
ggrant@upenn.edu
|
| Phone |
215-573-3736
|
| Organization name |
University of Pennsylvania
|
| Department |
Genetics
|
| Lab |
ITMAT Bioinformatics
|
| Street address |
3400 Civic Center Blvd.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE115916 |
Sex dependent compensatory mechanisms to preserve blood pressure homeostasis in PGI2 receptor deficient mice |
|
| Relations |
| BioSample |
SAMN19036890 |
| SRA |
SRX10808442 |
