|
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 |