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| Status |
Public on Apr 14, 2024 |
| Title |
TPE-1 |
| Sample type |
SRA |
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| Source name |
exosomes from transudative pleural effusion
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| Organism |
Homo sapiens |
| Characteristics |
tissue: exosomes
disease state: cardiac failure
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| Extracted molecule |
total RNA |
| Extraction protocol |
TBPE or TPE specimens were centrifuged at 300 g for 10 min at 4°C. The supernatant was taken and centrifuged at 10,000 g for 30 min at 4°C. Then the supernatant was ultracentrifuged at 100,000 g for 70 min at 4°C. The pellet was resuspended in PBS buffer and ultracentrifuged again at 100,000 g for 70 min. After ultracentrifugation, the pellet was suspended with 50 μl PBS buffer and saved at -80°C.
Libraries were prepared according to Small RNA Sample Pre Kit. Briefly, The special structure of the 3 'and 5' ends of Small RNA (the 5 'end has complete phosphate group and the 3' end has hydroxyl group) was used, and total RNA was used as the starting sample cDNA was synthesized by reverse transcription of Small RNA by adding connectors to both ends of the RNA.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
miRNA
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference,modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
For the samples with biological replicates:Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: miRNA expression levels were estimated byTPM (transcript per million) through the following criteria , Normalizationformula: Normalizedexpression=mappedreadcount/Totalreads*1000000
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| Submission date |
Apr 15, 2021 |
| Last update date |
Apr 14, 2024 |
| Contact name |
Li-Mei Liang |
| E-mail(s) |
d201881384@sina.com
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| Organization name |
Huazhong University of Science and Technology
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| Department |
Department of Respiratory and Critical Care Medicine, Union Hospital
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| Lab |
Key Laboratory of Respiratory Diseases, Ministry of Health of China
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| Street address |
1277 JieFang Avenue
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430030 |
| Country |
China |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE172150 |
Expression of miRNA in exosomes from transudative pleural effusion and tuberculous pleural effusions |
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| Relations |
| BioSample |
SAMN18747538 |
| SRA |
SRX10606484 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5242736_TPE-1.txt.gz |
6.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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