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| Status |
Public on Oct 19, 2022 |
| Title |
21 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
disease: Heart Failure Patients after Acute Myocardial Infarction
group: non sacubitril/valsartan resistance
cell type: PBMC
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| Extracted molecule |
total RNA |
| Extraction protocol |
After PBMC isolation, total RNA in samples were obtained by using TRIzol reagent, and the purity and concentration of them were determined with the instrument of NanoDrop ND-1000. If the OD was in the range of 1.8-2.0, the RNA was included in the follow-up experiment. According to rtStar tRF & tiRNA Pretreatment Kit protocols (Arraystar, USA), the total RNA samples were pretreated to remove RNA modifications
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
21
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| Data processing |
Trimmed reads (trimmed 5ÿ , 3ÿ -adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2
Based on alignment statistical analysis (mapping ratio, read length, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. If so, the expression profiling and differentially expressed tRFs & tiRNAs and miRNAs are calculated.
Principal Component Analysis (PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed for the expressed tRF & tiRNA in R or perl environment for statistical computing and graphics
Assembly: GtRNAdb (http://gtrnadb.ucsc.edu/) and tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/)
Supplementary files format and content: txt
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| Submission date |
Jul 11, 2022 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Jia Su |
| E-mail(s) |
nbsj54@126.com
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| Organization name |
Ningbo No. 1 Hospital
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| Street address |
Liuting Street No.59
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| City |
Ningbo |
| State/province |
China |
| ZIP/Postal code |
315010 |
| Country |
China |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE207882 |
tRNA-derived Small RNAs and their Potential Roles in the Therapeutic Heterogeneity of Sacubitril/valsartan in Heart Failure Patients after Acute Myocardial Infarction |
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| Relations |
| BioSample |
SAMN29630074 |
| SRA |
SRX16114089 |
| 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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