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| Status |
Public on Mar 14, 2018 |
| Title |
Circulating miRNAs. isomiRs and small RNA clusters in human plasma and breast milk |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Circulating small RNAs. including miRNAs but also isomiRs and other RNA species. have the potential to be used as non-invasive biomarkers for communicable and non-communicable diseases. This study aims to characterize miRNAs. isomiRs and small RNA clusters in biofluids. to compare their profiles. and to help in the establishment of standard guidelines. For this purpose. RNA from plasma and breast milk samples from 15 healthy postpartum mothers was extracted. Small RNA libraries were prepared with the NEBNext® small RNA library preparation kit and sequenced in an Illumina HiSeq2000 platform. After an initial quality control. miRNAs. isomiRs and clusters of small RNAs were annotated using seqBuster/seqCluster framework. The average amount of extracted RNA was 81 ng/mL [standard deviation (SD): 41] and 3985 ng/mL (SD: 3767) for plasma and breast milk. respectively. Mean number of good quality reads was 4.04 million (M) (40.01% of the reads) in plasma and 12.5M (89.6%) in breast milk. One thousand one hundred eighty two miRNAs. 74.317 isomiRs and 1.053 small RNA clusters that included piwi-interfering RNAs (piRNAs). tRNAs. small nucleolar RNAs (snoRNA) and small nuclear RNAs (snRNAs) were detected. Samples grouped by biofluid. with 308 miRNAs. 4.737 isomiRs and 778 small RNA clusters differentially detected. In summary. plasma and milk showed a completely different small RNA profile. In both. miRNAs. piRNAs. tRNAs. snRNAs. and snoRNAs were identified. confirming the presence of non-miRNA species in biofluids
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| Overall design |
Peripheral blood was collected at 0-48 h post-partum for 15 participants. only 5 samples of plasma pass QC; and breast milk was collected at 48-72 h post-partum for 10 of the participants
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| Contributor(s) |
Rubio M, Bustamante M, Hernandez-Ferrer C, Pantano L, Sarria Y, Piqué-Borras M, Vellve K, Agramunt S, Carreras R, Estivill X, Gonzalez JR, Mayor A |
| Citation(s) |
29505615 |
| |
| Submission date |
Nov 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lorena Pantano |
| E-mail(s) |
lpantano@iscb.org
|
| Organization name |
Harvard Chan School of Public Health
|
| Department |
Biostatistics
|
| Lab |
Bioinformatic Core
|
| Street address |
655 Huntington Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA420449 |
| SRA |
SRP125870 |
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