|
Status |
Public on May 07, 2021 |
Title |
Atria_DKO_Female_F8 |
Sample type |
SRA |
|
|
Source name |
heart atria
|
Organism |
Mus musculus |
Characteristics |
tissue: heart atria genotype: Ipr/Ldlr DKO gender: female library barcode: GGACTTGG-CGCAGACG
|
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.
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|
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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.
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|
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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 |
SAMN19036895 |
SRA |
SRX10808439 |