|
| Status |
Public on Sep 18, 2013 |
| Title |
optimized ligation for synthetic miRs with worm total RNA, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
chemically synthesized miRNAs
|
| Organism |
Mus musculus |
| Characteristics |
sample type: synthetic miRNAs
|
| Growth protocol |
Mice were housed in the Mouse Facility under standard conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells with the use of Trizol according to the Trizol manufacturer's instructions. Synthetic miRNAs were chemically synthesized by ThermoFisher according to published mouse miRNA sequences.
An improved Ligation-based small RNA cloning protocol based on the Illumina protocol for small RNA cloning. Two adaptors (3' adaptor and 5' adaptor) were ligated to small RNAs followed by RT-PCR and gel-purification. Then purified PCR products were sent out for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
no barcode
|
| Data processing |
adaptor removal with self-written python scripts
miRNA mapping with BLAST, parameters: -m 8
BLAST results parsing and miRNA counts with self-written python scripts
Genome_build: Mouse miRNA sequences from Mirbase.org
Supplementary_files_format_and_content: .xls file containing counts assigned to each miRNA
|
| |
|
| Submission date |
Jun 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhaojie Zhang |
| E-mail(s) |
Zhaojie.Zhang@colorado.edu
|
| Organization name |
University of Colorado at Boulder
|
| Street address |
2300 Arapahoe Ave
|
| City |
Boulder |
| State/province |
CO |
| ZIP/Postal code |
80302 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE47858 |
High-efficiency RNA cloning enables quantitative measurement of miRNA expression by deep sequencing |
|
| Relations |
| BioSample |
SAMN02202300 |
| SRA |
SRX304993 |
