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| Status |
Public on Mar 07, 2017 |
| Title |
control_group_time_1_subject_5 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
time: baseline
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| Extracted molecule |
total RNA |
| Extraction protocol |
Blood samples were collected into PAXgene blood RNA tubes and processed with PAXgene blood miRNA kit (Qiagen, Valencia, CA) for miRNA extraction. Quality and quantity of extracted RNA was assessed using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and the Agilent Bioanalyzer 2100 Small RNA assay (Agilent Technologies, Inc., Santa Clara, CA). All samples were enriched for miRNA using standard recommendations for preparation of small RNA libraries protocol.
Barcoded libraries were prepared with an input of 1-5ng of enriched small RNA using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA). Template-positive Ion PGM™ Ion Sphere™ Particles were prepared for sequencing using Ion PGM™ Template OT2 200 Template Kit v2 with pooled libraries optimized to 14pM.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
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| Description |
Ion Torrent PGM with the Ion 316 Chip v2
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| Data processing |
Sequencing reads were generated and initially processed by Ion Torrent Suite software version 4.4.2.
Low quality reads and polyclonal sequences were filtered from sequencing data, then raw data was trimmed to 22 base pairs from 5’ end and profiles were generated by aligning sequences to hg19 with BWA; then, we quantified using miRDeep2 v2.0.0.7 and annotated based on miRBase v20.
Differential expression analysis was conducted on DESeq2 with Benjamini and Hochberg multiple testing correction applied.
Target prediction and analysis was conducted using the miRWalk2.0 database.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts
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| Submission date |
Oct 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sijung Yun |
| Organization name |
NIH/JHU
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| Street address |
8908 Ewing Drive
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20817 |
| Country |
USA |
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| Platform ID |
GPL17301 |
| Series (1) |
| GSE87768 |
Circulating miRNA Associated with Posttraumatic Stress Disorder in a Cohort of Military Combat Veterans |
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| Relations |
| BioSample |
SAMN05880414 |
| SRA |
SRX2229938 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2340044_miRNAs_expressed_control_group_time_1_subject_5.csv.gz |
15.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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