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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 14, 2018 |
| Title |
Subject14_milk |
| Sample type |
SRA |
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| Source name |
Breast milk
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| Organism |
Homo sapiens |
| Characteristics |
age (years): 35
region of origin: Asia
parity: 2
rna concentration (ng/ml): 4986.67
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| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs were extracted using the miRNeasy Serum/Plasma kit (Qiagen, Cat No.: 217184) with minor modifications. RNA extraction was performed from at least 3 mL of plasma and milk. One mL of biofluid was filtered per each column and washed two times with ethanol 80% before elution
Libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible) (NEB, Cat No.: E7330) following manufactures instructions and using 150ng of RNA obtained from plasma samples and 500 ng from milk. Library size selection was done using acrylamide gels.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
An initial QC was conducted using FASTX-Toolkit and FastQ Screen. After adaptor removal, reads with the following features were removed: 1) Reads <18nt, 2) Mean PHRED scores < 30, and 3) Low complexity reads based on mean score of the read
Sequences fulfilling QC were used as the input of the seqBuster/seqCluster tool that retrieves three matrices of counts: i) miRNA, ii) isomiRs, and iii) small RNA clusters
In order to detect miRNAs and isomiRs, reads were mapped to hairpins released from miRBasev21 using miraligner
In parallel, sequences were mapped to hs37d5 using bowtie, and hotspots (sets of overlapping sequences according to their position in the genome) were detected
Hotspots sharing any sequence were grouped in primary clusters. Then, a recursively heuristic algorithm based on reduction and cluster correction was applied to the ones sharing over 60% of the sequences. These were annotated to different RNA species using miRBase v20, refGene (RefSeq genes), wgRna (CD and H/ACA Box snoRNAs and miRNAs from Weber and Griffiths-Jones), rmsk (Repeating elements created using RepeatMasker) and tRNA from University of California Santa Cruz (UCSC) genome browser (hg19), and piR_hg19_v1.0 from the regulatoryrna database (www.regulatoryrna.org).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of unnormalized counts per gene
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| Submission date |
Nov 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lorena Pantano |
| E-mail(s) |
lpantano@iscb.org
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| Organization name |
Harvard Chan School of Public Health
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| Department |
Biostatistics
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| Lab |
Bioinformatic Core
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| Street address |
655 Huntington Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE107524 |
Circulating miRNAs. isomiRs and small RNA clusters in human plasma and breast milk |
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| Relations |
| BioSample |
SAMN08113296 |
| SRA |
SRX3432760 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2870522_M14.fasta.gff.gz |
299.2 Kb |
(ftp)(http) |
GFF |
| GSM2870522_M14_cluster.csv.gz |
3.5 Kb |
(ftp)(http) |
CSV |
| GSM2870522_M14_isomir.csv.gz |
47.0 Kb |
(ftp)(http) |
CSV |
| GSM2870522_M14_mir.csv.gz |
4.8 Kb |
(ftp)(http) |
CSV |
| GSM2870522_M14_trna.csv.gz |
89.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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