|
| Status |
Public on Jul 31, 2015 |
| Title |
serum miRNA from alcohol use disorder subject replicate 15 [miRNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood serum
|
| Organism |
Homo sapiens |
| Characteristics |
broad diagnosis: alcohol use disorder
narrow diagnosis: alcohol dependence
age (years): 23
Sex: Male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen total RNA
RNA libraries were prepared for sequencing using Illumina TruSeq small RNA protocol
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
miRNA expression data from the peripheral blood serum
14-322
|
| Data processing |
After phasing, prephasing, normalization and cross talk correction are taken into account, base calling was performed by Illumina Real Time Analysis (RTA) software (version 1.17.28) on the MiSeq instrument
Sequenced reads were trimmed for adaptor sequence, FASTQ files were subsequently imported into Partek Flow and Strand NGS suites for alignment and analysis. Base calls below a phred score of 20 were trimmed. Reads were aligned to the human hg19 reference genome using the Bowtie algorithm. These were then quantified against both miRBase (version 20) and RefSeq transcript miRNA annotations (4-29-14). Any miRNAs that were detected in fewer than 5 human subjects were discarded from further analysis. Raw miRNA counts were then normalized to the total number of miRNA reads per sample and expressed as a percentage of that total.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include percent of total read values for each sample
|
| |
|
| Submission date |
Jul 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Frank A Middleton |
| E-mail(s) |
middletf@upstate.edu
|
| Phone |
315-464-7721
|
| Organization name |
SUNY Upstate Medical Univ
|
| Department |
Neuroscience and Physiology
|
| Street address |
505 Irving Avenue
|
| City |
Syracuse |
| State/province |
NY |
| ZIP/Postal code |
13210 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (2) |
| GSE71578 |
Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain [miRNA-Seq] |
| GSE71579 |
Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain |
|
| Relations |
| BioSample |
SAMN03945380 |
| SRA |
SRX1125870 |
