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| Status |
Public on Nov 28, 2024 |
| Title |
sprague-Dawley,phosphatase inhibitor Lats-1,Day7_y5 |
| Sample type |
SRA |
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| Source name |
myocardium
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: myocardium
strain: sprague-Dawley
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| Extracted molecule |
total RNA |
| Extraction protocol |
①RNA degradation and contamination was monitored on 1% agarose gels. ② RNA purity was checked using the NanoPhotometer ®spectrophotometer(IMPLEN, CA, USA) . ③ RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system(Agilent Technologies, CA, USA）.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Quality control, Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Novel transcripts prediction.The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package
GO and KEGG enrichment analysis of differentially expressed genes
Assembly: Rattus_norvegicus.Rnor_6.0.97
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Dec 05, 2023 |
| Last update date |
Nov 28, 2024 |
| Contact name |
min wang |
| E-mail(s) |
[email protected]
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| Organization name |
Affiliated Suzhou Hospital of Nanjing Medical University
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| Street address |
242 Guangji Road
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| City |
Suzhou |
| ZIP/Postal code |
215008 |
| Country |
China |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE249368 |
Connexin 43 dephosphorylation mediates the Dchs1/YAP/TEAD signaling pathway to impact cardiac fibrosis |
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| Relations |
| BioSample |
SAMN38689678 |
| SRA |
SRX22795109 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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