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| Status |
Public on Jul 03, 2024 |
| Title |
Nitrofen_No-CDH_fetal-lung_4 |
| Sample type |
SRA |
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| Source name |
fetal lung
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| Organism |
Rattus norvegicus |
| Characteristics |
embryonic day: 21
tissue: fetal lung
treatment: Nitrofen
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| Treatment protocol |
Two rats received 100 mg of nitrofen (2,4-dichlorophenyl-p-nitrophenylether) dissolved in 1 mL of olive oil and one rat received olive oil alone through the gastric tube on pregnancy day 9.
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| Growth protocol |
Three pregnant Sprague-Dawley rats were purchased from Japan SLC Inc. (Hamamatsu, Japan). All rats were maintained on a 12 h light/ 12 h dark lighting schedule (lights on 9:00 a.m., off at 9:00 p.m.), and allowed free access to water and standard chow.
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| Extracted molecule |
total RNA |
| Extraction protocol |
On day 21 of the pregnancy, the rats were sacrificed. After uterine incision, amniotic fluid was collected using cellulose nanofiber-based EV sheets. we checked for the presence of a diaphragm in all fetuses by thoracolaparotomy. Next, lung tissues were collected in GentleMACS M tubes (Miltenyi Biotec, Bergisch Gladbach, Germany) containing 1.5 mL of QIAzol buffer (Qiagen, Hilden, Germany). Total RNA was extracted using the miRNeasy 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 |
Illumina MiSeq |
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| Description |
processed_data_rat-Lung.txt
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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 base mismatches.
Assembly: miRbase 21
Supplementary files format and content: txt files of raw read counts of each samples
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| Submission date |
Aug 10, 2023 |
| Last update date |
Jul 03, 2024 |
| 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 |
GPL19052 |
| Series (1) |
| GSE240558 |
The miRNA profiles of amniotic fluid-derived extracellular vesicles and fetal lung tissue of nitrofen-induced congenital diaphragmatic hernia rat model. |
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| Relations |
| BioSample |
SAMN36948601 |
| SRA |
SRX21326040 |
| 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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