|
| Status |
Public on Aug 28, 2018 |
| Title |
605044 [miRNA] |
| Sample type |
SRA |
| |
|
| Source name |
stem
|
| Organism |
Mus musculus |
| Characteristics |
tissue: stem
age: 6 month
strain: FVB
transgenic: Wt
rin: 8.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using miRNeasy kit, Qiagen following manufacture's protocol
RNA libraries were prepared for sequencing using Standard miRNA sequencing kit, Illumina
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Different brain regions were isolated from F1 hybrids of TPR50 tau Transgenic mice crossed with DBA, FVB and C57BL6 strains and run for miRNA sequencing
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, mapped and annotated using mirDeep2 package
Counts were estimated using mirDeep2 package
Normalized counts were estimated using miRDeep2 package. Only those miRNAs were used which had at least 10 counts in 80% of samples
Genome_build: miRbase 20, NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include Normalized log2 counts values for each Sample ...
|
| |
|
| Submission date |
Nov 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Vivek Swarup |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California Irvine
|
| Department |
Neurobiology and Behavior
|
| Street address |
3400 Bio Sci 3
|
| City |
Irvine |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE89983 |
microRNA-seq of TPR50 Tau P301S Transgenic Mouse in different brain regions and time-points |
| GSE90696 |
Identification of evolutionary conserved gene networks that mediate neurodegenerative dementia |
|
| Relations |
| BioSample |
SAMN06030530 |
| SRA |
SRX2356270 |
