|
| Status |
Public on May 31, 2020 |
| Title |
An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits |
| Organisms |
Homo sapiens; synthetic construct |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
We compared the performance of two commercial kits (NEBNext and NEXTflex) for miRNA detection sensitivity, reliability, titration response and ability to detect differentially expressed miRNAs at different amounts of synthetic miRNAs. We observed differences in detection sensitivity between the kits, but none were able to detect the full repertoire of expected miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the majority of miRNAs. In a previous publication (https://doi.org/10.1080/15476286.2019.1667741; GEO accession number GSE133719) we accessed the performance of six additional miRNA library preparation kits.
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| Overall design |
Systematic comparison of miRNA profiles assessed in low-input synthetic miRNA samples and samples from pools of blood derived CD8 T cells of rheumatoid arthritis (RA) patients or healthy controls (HC) by six commercially available library preparation kits. In a previous publication (https://doi.org/10.1080/15476286.2019.1667741; GEO accession number GSE133719) we accessed the performance of six additional miRNA library preparation kits.
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| |
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| Contributor(s) |
Heinicke F, Gilfillan GD |
| Citation(s) |
32436772 |
| |
| Submission date |
Dec 09, 2019 |
| Last update date |
Nov 02, 2020 |
| Contact name |
Fatima Heinicke |
| E-mail(s) |
fatima.heinicke@gmail.com
|
| Organization name |
Oslo University Hospital
|
| Department |
Department of Medical Genetics
|
| Street address |
Kirkeveien 166
|
| City |
Oslo |
| ZIP/Postal code |
0450 |
| Country |
Norway |
| |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL19604 |
Illumina HiSeq 2500 (synthetic construct) |
|
| Samples (42)
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| Relations |
| BioProject |
PRJNA594317 |
| SRA |
SRP235240 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE141658_Composer.biologic.matureRef.fasta.gz |
28.5 Kb |
(ftp)(http) |
FASTA |
| GSE141658_Composer.synthetic.matureRef.fasta.gz |
11.0 Kb |
(ftp)(http) |
FASTA |
| GSE141658_countTable_biological.csv.gz |
21.5 Kb |
(ftp)(http) |
CSV |
| GSE141658_countTable_biological_downsampled.csv.gz |
13.8 Kb |
(ftp)(http) |
CSV |
| GSE141658_countTable_biological_rlog_downsampled.csv.gz |
80.0 Kb |
(ftp)(http) |
CSV |
| GSE141658_countTable_synthetic.csv.gz |
67.7 Kb |
(ftp)(http) |
CSV |
| GSE141658_countTable_synthetic_downsampled.csv.gz |
54.7 Kb |
(ftp)(http) |
CSV |
| GSE141658_countTable_synthetic_rlog_downsampled.csv.gz |
157.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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