|
| Status |
Public on May 20, 2021 |
| Title |
miRXplore_mDOT-seq 1U_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
miRXplore Universal Reference (Miltenyi Biotec)
|
| Organism |
synthetic construct |
| Characteristics |
source: miRXplore Universal Reference (Miltenyi Biotec)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRXplore Universal Reference (Miltenyi Biotec) RNA was denaturated in the presence of EDTA, modified with azide group and 3' alkyne-adapter/RT primer via the click reaction. The resulting RNA-DNA conjugate was used for RNA library preparation according to the NEXTflex Small RNA-seq Kit v3 (PerkinElmer) starting from Step B with the following modifications: at Step D ¼ dilution of NEXTflex 5' 4N adapter was used, at Step G 18 cycles of PCR were performed and Step H1 was proceeded with Step H2.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
1U_2
|
| Data processing |
Reads were filtered by length and presence of the adaptors using cutadapt (-m 10 --discard-untrimmed –max-n 0) and later deduplicated using custom Unix script.
To count the reads corresponding to each miRNA, custom reference libraries were created using an in-house Unix script and miRNAs counted by exact match.
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for all samples.
|
| |
|
| Submission date |
Feb 17, 2021 |
| Last update date |
May 20, 2021 |
| Contact name |
Kotryna Kvederaviciute |
| E-mail(s) |
kotryna.kvederaviciute@mif.vu.lt
|
| Organization name |
Vilnius University
|
| Department |
Life Sciences Center
|
| Lab |
Institute Of Biotechnology
|
| Street address |
Sauletekio av. 7
|
| City |
Vilnius |
| ZIP/Postal code |
10257 |
| Country |
Lithuania |
| |
|
| Platform ID |
GPL27609 |
| Series (2) |
| GSE166931 |
Sequencing of miRXplore Universal Reference (Miltenyi Biotec) RNA using mDOT-seq |
| GSE166932 |
Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAs in probiotic Lactobacillus casei |
|
| Relations |
| BioSample |
SAMN16911515 |
| SRA |
SRX9609778 |
