|
| Status |
Public on Aug 05, 2015 |
| Title |
pooled lung tissue miRNA from 3 non-drinking male adolescent control rats |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: lung
age: postnatal day 35
Sex: male
treatment: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen total RNA
RNA libraries were prepared for sequencing using Illumina TruSeq small RNA protocol
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
miRNA expression data from untreated male control rats
|
| 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 for alignment and analysis. Base calls below a phred score of 20 were trimmed. Reads were aligned to the rat Rn5 reference genome using the Bowtie algorithm. These were then quantified against both Precursor and Mature miRBase (version 21) sequences and RefSeq transcript miRNA annotations (7-30-14). Raw miRNA counts are reported.
Genome_build: Rn5
Supplementary_files_format_and_content: tab-delimited text files include percent of total read values for each sample
|
| |
|
| Submission date |
Aug 04, 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 |
GPL19052 |
| Series (2) |
| 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 |
| GSE71697 |
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 [rat miRNA-Seq] |
|
| Relations |
| BioSample |
SAMN03955878 |
| SRA |
SRX1131897 |
