|
| Status |
Public on May 15, 2015 |
| Title |
Illumina_v1v2_adaptors |
| Sample type |
SRA |
| |
|
| Source name |
miRXplore Universal Reference
|
| Organism |
synthetic construct |
| Characteristics |
substrate: RNA oligonucleotides
3' adaptor: Ill MidRand v1+v2
5' adaptor: Ill MidRand v1+v2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were synthesized oligonucleotides
Protocol was adapted from the NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs, Inc.). Adapters and primers were substituted as needed to meet the needs of the study
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
processed data file: UniversalReferenceRawReads.txt
|
| Data processing |
Adapter sequences were trimmed from the raw files using Galaxy (http://galaxyproject.org)
Trimmed sequences were annotated using Genomics Workbench 5.1 (CLC bio, Cambridge, MA) with a zero mismatch tolerance and a text file containing the sequences present in the mixture was used as the annotation reference.
Genome_build: not applicable
Supplementary_files_format_and_content: Text files were generated from Galaxy [N21_primarysequence.txt], the output of Genomics Workbench 5.1 annotation results [UniversalReferenceRawReads.txt, OligoMixesRawReads.txt] or RNA CONTRAfold (http://contra.stanford.edu/contrafold/index.html) [N21_CONTRAfold] or Vienna RNAcofold (http://rna.tbi.univie.ac.at/cgi-bin/RNAcofold.cgi) [N21_cofold] results.
more details provided in the 'readme.txt'
|
| |
|
| Submission date |
Mar 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Timothy Fuchs |
| E-mail(s) |
fuchs@neb.com
|
| Phone |
6145797408
|
| Organization name |
New England Biolabs
|
| Department |
RNA Biology
|
| Street address |
240 County Road
|
| City |
Ipswich |
| State/province |
MA |
| ZIP/Postal code |
01938 |
| Country |
USA |
| |
|
| Platform ID |
GPL17769 |
| Series (1) |
| GSE67053 |
Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure |
|
| Relations |
| BioSample |
SAMN03433332 |
| SRA |
SRX959196 |
