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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 04, 2024 |
| Title |
mouse, feces, C4 |
| Sample type |
SRA |
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| Source name |
feces
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| Organism |
Mus musculus |
| Characteristics |
tissue: feces
condition: Control
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135 155 bp PCR amplified fragments (corresponding to 15 35 nt small RNAs).
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads were normalized by calculated CPM value
Differential expression analysis of miRNAs between groups was performed using edgeR with settings of 1.5-fold difference, p-value < 0.05 and within-group CPM mean of 1 to screen for differentially expressed miRNAs.
Assembly: mm10
Supplementary files format and content: Microsoft excel file includes the counts per million (CPM) reads of miRNAs in all samples.
Supplementary files format and content: Differential expression analysis of miRNAs between groups was performed using edgeR. For differentially expressed miRNA were screened with the significant threshold to 1.5-fold difference, p-value ≤ 0.05 and the mean CPM within the group ≥ 1
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| Submission date |
Feb 28, 2024 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Hong xu Liu |
| E-mail(s) |
qinnb@dlpu.edu.cn
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| Phone |
13147746039
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| Organization name |
Dalian Polytechnic University
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| Street address |
1 Light Industry Garden, Ganjingzi District, Dalian City, Liaoning Province, China
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| City |
Dalian |
| ZIP/Postal code |
116000 |
| Country |
China |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE260446 |
Polysaccharides from Sargassum fusiforme protect mice against Citrobacter rodentium infection through intestinal microbiota-drived microRNA-92a-3p |
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| Relations |
| BioSample |
SAMN40186762 |
| SRA |
SRX23776887 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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