|
| Status |
Public on Jul 23, 2012 |
| Title |
N21-HD-r2 |
| Sample type |
SRA |
| |
|
| Source name |
Random oligo, 21 nucleotides
|
| Organism |
synthetic construct |
| Characteristics |
adapters: HD
length: 21
molecule: Random oligo, 21 nucleotides
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For N9 RNA and N21 RNA cloning for NGS approximately 3 and 100 pmoles of oligonucleotide were used respectively. Library preparation was based on the Illumina small RNA v1.5 sample preparation guide. RNA was ligated to the pre-adenylated 3' adapter (custom synthesised by Bioo Scientific) with T4 Rnl2 truncated ligase (NEB). The ligated fragment was then ligated to the 5' adapter (Dharmacon) using T4 Rnl1. For Illumina protocol recommended adapter sequences were used. For HD protocol four degenerate nucleotides (with uniform probability distribution) were added both to the 5' end of the 3' adapter and to the 3 end of the 5' adapter. The ligated fragment was then reverse transcribed using the SRA RT primer followed by 8-14 cycles of PCR. The PCR products were size fractionated by polyacrylamide gel electrophoresis (8% PAGE). A band corresponding to approximately 100bp was gel purified and sent for NGS sequencing on a Illumina Genome Analyzer IIx with 50 nt read length (Baseclear).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Random oligo, 21 nucleotides, HD protocol, replicate 2
|
| Data processing |
3' adapter was trimmed, reads summarized after adapter trimming
|
| |
|
| Submission date |
Mar 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Helio Pais |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oxford
|
| Department |
Weatherall Institute of Molecular Medicine
|
| Street address |
Jonh Radcliffe Hospital
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9423 |
| Series (1) |
| GSE36540 |
Sequencing random oligonucleotides using standard GA II protocol |
|
| Relations |
| SRA |
SRX129975 |
| BioSample |
SAMN00828819 |
