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| Status |
Public on Jul 14, 2021 |
| Title |
miRNA_PD_01 |
| Sample type |
SRA |
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| Source name |
Colonic biopsy
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| Organism |
Homo sapiens |
| Characteristics |
group: Patient with Parkinson's disease
disease: Patient with Parkinson's disease
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| Extracted molecule |
total RNA |
| Extraction protocol |
Biopsies of the in the sigmoid colon were taken during colonoscopy and subsequently cryoconserved. In order to assess tissue-specific miRNA expression, the biopsies were micro-dissected prior to preservation. Total RNA was extracted using TRIzol reagent according to the instructions of the manufacturer.
Sequencing libraries were prepared using NEXTflex Small RNA Seq Kit v 3 (Bio Scientific) according to the small RNA protocol of the manufacturer.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 550 |
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| Description |
DE_disease.csv
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| Data processing |
Fastq-files were generated using Illumina bcl2fastq (v2.20.0.422).
Bioinformatic analyses were performed according to Stokowy et al. (Stokowy T, Eszlinger M, Swierniak M, Fujarewicz K, Jarzab B, Paschke R, Krohn K. Analysis options for high-throughput sequencing in miRNA expression profiling. BMC research notes. 2014;7:144).
Mapping against miRBase release 22 reference sequences was done using Bowtie2.
Differential expression was analyzed using DESeq2.
Genome_build: miRBase (release 22)
Supplementary_files_format_and_content: CSV-files (comma-separated values) containing differential expression datasets.
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| Submission date |
Feb 24, 2020 |
| Last update date |
Jul 14, 2021 |
| Contact name |
Bernd Henrik Northoff |
| E-mail(s) |
[email protected]
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| Organization name |
Ludwig-Maximilians-University Munich
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| Department |
Institute of Laboratory Medicine
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| Street address |
Marchioninistr. 15
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| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE145814 |
Differential expression of gut miRNAs in idiopathic Parkinson's disease |
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| Relations |
| BioSample |
SAMN14170326 |
| SRA |
SRX7789757 |
| 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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