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| Status |
Public on Oct 18, 2017 |
| Title |
Patient_25 |
| Sample type |
SRA |
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| Source name |
Plasma
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| Organism |
Homo sapiens |
| Characteristics |
Sex: FEMALE
age: 46
neuropathy (yes: 1/no:0): 1
cardiopathy (yes: 1/no:0): 1
diabetes (yes: 1/no:0): 0
gaa repetitions (allele1/allele2): 767/767
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| Extracted molecule |
total RNA |
| Extraction protocol |
blood samples were collected in EDTA tubes and centrifuged at 2500 rpm for 10 minutes. Once plasma was obtained, each sample was stored at −80°C until RNA extraction. 500 µL of plasma were used to isolate cell-free total RNA (including miRNAs) using the miRNeasy Serum/Plasma kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol.
RNA libraries were prepared with NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1&2), and they were sequenced using standard Illumina protocols.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
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| Description |
counts_rawData.txt
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| Data processing |
Sequenced reads were trimmed for adaptor sequence and filtered by size and quality using Cutadapt
The remaining sequences were aligned to the human genome reference (Hg38) from the UCSC Genome Browser using the Subread package in Linux
The expression of every miRNA per sample was measured using the annotation file with mature miRNAs from miRBase (v21) and the R package Rsubread.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts of sequencing reads of every miRNA per sample
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| Submission date |
Oct 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Marta Seco-Cervera |
| E-mail(s) |
marta.seco@uv.es
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| Organization name |
University of Valencia
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| Street address |
Av Blasco Ibañez, 15
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| City |
Valencia |
| ZIP/Postal code |
46393 |
| Country |
Spain |
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| Platform ID |
GPL15456 |
| Series (1) |
| GSE105052 |
Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients |
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| Relations |
| BioSample |
SAMN07795847 |
| SRA |
SRX3292421 |
| 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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