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Sample GSM7946892 Query DataSets for GSM7946892
Status Public on Jan 17, 2024
Title HFpEF + Veh_2307
Sample type SRA
 
Source name Left ventricle
Organism Mus musculus
Characteristics tissue: Left ventricle
disease state: HFD/L-NAME HFpEF model
genotype: WT
strain: C57BL6
treatment: Vehicle
Treatment protocol HFD+L-NAME mice were randomized to different groups to receive oral doses of 15 mg/kg TYA-018 or vehicle (5% DMSO + 45% PEG-300 + 50% purified water) at 10 mL/kig once per day for 6-9 weeks. TYA-018 was formulated in vehicle.
Extracted molecule polyA RNA
Extraction protocol Approximately 106 cells or 20-30 mg of mouse heart tissue were lysed with TRI Reagent (Zymo Research) and frozen at -80 °C to ensure complete cell lysis. Total RNA was extracted and washed from lysed cells using the Direct-zol-96 RNA Kit (Zymo Research) according to the manufacturer’s instructions. Samples were treated with DNase I for 15 min at room temperature. cDNA was reverse transcribed from approximately 1 μg of RNA through random hexamers using the SuperScript III First-Strand Synthesis System according to the manufacturer’s instructions (Thermo Fisher Scientific). Real-time qPCR reactions were performed using the TaqMan universal PCR master mix (Thermo Fisher Scientific) with the TaqMan probes listed. RT-qPCR reactions were performed using the QuantStudio7 Flex Real-Time PCR systems (Thermo Fisher Scientific). Each reaction was performed in triplicate for a given RT-qPCR run, and each condition had four experimental replicates. Relative expression of the gene of interest was normalized to GAPDH as the housekeeping control using the 2–ΔΔCT method. P values were calculated with Student’s t-tests.
From each replicate, 100 ng total RNA was extracted via the polyA-tail-specific protocol according to Illumina, Inc.. The RNA libraries were prepared using a TruSeq Stranded mRNA kit (Illumina), which also removes ribosomal RNA. The libraries were sequenced as 100 base pair single-end reads using Illumina NovaSeq SP with an average of 29.8 million reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description TNYA0040_study
Data processing Adapter trimming by FASTP (ver. 0.23.2)
Read alignment by Salmon (ver. 1.6.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: hg38 v.13
Supplementary files format and content: TXT
 
Submission date Dec 05, 2023
Last update date Jan 17, 2024
Contact name Farshad Farshidfar
E-mail(s) ffarshidfar@tenayathera.com
Organization name Tenaya Therapeutics Inc.
Street address 171 Oyster Point Blvd Ste 500
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
 
Platform ID GPL24247
Series (2)
GSE249411 Bulk RNA-seq comparison of TYA018 HDAC6 inhibition vs vehicle after a single dose treatment in Mus Musculus to treat heart failure with preserved ejection fraction
GSE249414 Targeting HDAC6 to treat heart failure with preserved ejection fraction (HFpEF)
Relations
BioSample SAMN38679039
SRA SRX22788452

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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