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| Status |
Public on Apr 18, 2024 |
| Title |
Set7KO_ISO_2-A-161 |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Mus musculus |
| Characteristics |
tissue: Heart
genotype: Set7KO
treatment: isoproterenol (60mg/kg )
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the heart was isolated (TRIzol® Reagent, Invitrogen)
The sequencing libraries were obtained by the TruSeq Stranded mRNA Library Prep (Illumina).
The libraries were sequenced in the Illumina Nextseq platform using NextSeq 500 High Output Kit v2.5, 1x75 cycles, following the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
2-A-161-Index4_S2
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| Data processing |
The gene expression levels were measured by HISAT2 (ref: Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019). using the mouse reference transcriptome from GENCODE (GRCm38 Ensembl release 102; https://www.gencodegenes.org/).
Transcript assembly and quantification was performed using the StringTie (ref:. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT & Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 2015, doi:10.1038/nbt.3122)
The gene expression matrix generated was used as the input to perform differential expression analysis using edgeR (ref: McCarthy DJ, Chen Y, Smyth GK (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), 4288-4297. Doi: 10.1093/nar/gks042.)
Assembly: GRCm38 Ensembl release 102
Supplementary files format and content: raw count
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| Submission date |
Jul 06, 2022 |
| Last update date |
Apr 18, 2024 |
| Contact name |
Da-Zhi Wang |
| E-mail(s) |
dazhiw@usf.edu
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| Organization name |
University of South Florida
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| Department |
Center for Regenerative Medicine
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| Street address |
560 Channelside Dr, MDD 730
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| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33602 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE207581 |
Set7 deletion attenuates isoproterenol-induced cardiac fibrosis and prevents heart failure |
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| Relations |
| BioSample |
SAMN29538358 |
| SRA |
SRX16041807 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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