|
| Status |
Public on May 17, 2024 |
| Title |
shHmbox1_IRI_3 |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Mus musculus |
| Characteristics |
tissue: heart
genotype: WT(C57BL/6J)
treatment: AAV9-sh-Hmbox1
|
| Treatment protocol |
Pre-treatment with sh-Hmbox1 AAV9 or control AAV9 vectors via tail vein 1 week before I/R or sham surgery
|
| Growth protocol |
Male C57BL/6J mice of eight-to-ten weeks old were purchased from Charles River (Beijing, China) and maintained in SPF laboratory animal facility. Mice were fed a standard diet for 1 week of adaptive feeding.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's instructions.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The transcriptome sequencing was performed on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the mm14 genome using HISAT2.
FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
DESeq2 was used for gene expression analysis.
|
| |
|
| Submission date |
Aug 17, 2023 |
| Last update date |
May 17, 2024 |
| Contact name |
Yujiao Zhu |
| E-mail(s) |
zhu1yu2jiao3@i.shu.edu.cn
|
| Phone |
18817602272
|
| Organization name |
Shanghai University
|
| Street address |
Nanchen Road 381
|
| City |
shanghai |
| ZIP/Postal code |
200044 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE241079 |
Role of reducing Hmbox1 in cardiac ischemia/reperfusion injury |
|
| Relations |
| BioSample |
SAMN37037107 |
| SRA |
SRX21393059 |
