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| Status |
Public on Oct 03, 2023 |
| Title |
Pt4_tumor-surface1 |
| Sample type |
SRA |
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| Source name |
primary cancer
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| Organism |
Homo sapiens |
| Characteristics |
type: EV
location: surface
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| Extracted molecule |
total RNA |
| Extraction protocol |
The EV sheet was fabricated from cellulose nanofibers. The EV capture process from moistened organs using the EV sheet consists of the following steps: EV capture by absorption of ascites on organs, EV storage by drying, washing, and EV release. Then, total RNA was extracted using RNA purification kit (Norgen Biotek Corp, Thorold, Canada). To obtain tissue RNA, tissues were shredded using the gentleMACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) and total RNAs was extracted by using the miRNeasy Plus Mini Kit (QIAGEN, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 550 |
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| Description |
ICA001-07328A-001-E10-C01-NGS001_S10_L001_R1_001
Pt4_data file(RPM).xlsx
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| Data processing |
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to the miRbase 21 database allowing up to two mismatches
Reads per million mapped reads (RPM) method was used for normalization.
Assembly: miRbase 21
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| Submission date |
Oct 27, 2022 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Kosuke Yoshida |
| E-mail(s) |
yoshida.kousuke@med.nagoya-u.ac.jp
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| Organization name |
Nagoya University
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| Street address |
65 Tsuruma-cho
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| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
466-8550 |
| Country |
Japan |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE216745 |
Spatial extracellular vesicle microRNA profiles in ovarian cancer |
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| Relations |
| BioSample |
SAMN31493529 |
| SRA |
SRX18050742 |
| 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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