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| Status |
Public on Aug 25, 2023 |
| Title |
Urinary exosome, ultra-high speed centrifugation [C3] |
| Sample type |
SRA |
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| Source name |
Urinary exosome
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Urinary exosome
subject status: normal subjects
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| Extracted molecule |
other |
| Extraction protocol |
Urine was mixed with RiboTM Exosome Isolation Reagent and exosome isolation was performed according to the manufacturer’s instructions (Ribobio, China). Exosomal RNA was extracted by HiPure Liquid miRNA Kit/HiPure Serum/Plasma miRNA Kit (Megan, China).
Exosomal RNA were used to prepare small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB,USA) according to manufacturer’s instructions
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
*library strategy: exosome sRNA-seq
Illumina Bcl2FastQ software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the human reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Assembly: hg19
Supplementary files format and content: \06.know_miRNA_expression\*\*.miR.expre.xls
Supplementary files format and content: \11.differential_expression\*\**vs*.diff.xls
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| Submission date |
Aug 21, 2023 |
| Last update date |
Aug 25, 2023 |
| Contact name |
Wei Zhu |
| Organization name |
The First Affiliated Hospital of Guangzhou Medical University
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| Street address |
No.1 Kangda Road, Haizhu District, Guangzhou City, Guangdong Province
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| City |
Guangzhou |
| ZIP/Postal code |
510230 |
| Country |
China |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE241241 |
MiR-148b-5p promotes hypercalciuric kidney stone formation via regulating circRNA-83536/miR-24-3p/Calcitonin Receptor signaling [exosome-miR-seq] |
| GSE241243 |
MiR-148b-5p promotes hypercalciuric kidney stone formation via regulating circRNA-83536/miR-24-3p/Calcitonin Receptor signaling |
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| Relations |
| BioSample |
SAMN37071984 |
| SRA |
SRX21431395 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7719886_C3.base.bias.txt.gz |
351 b |
(ftp)(http) |
TXT |
| GSM7719886_C3.miR.expre.txt.gz |
9.8 Kb |
(ftp)(http) |
TXT |
| GSM7719886_C3.miRNA.length.txt.gz |
135 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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