|
| Status |
Public on May 15, 2013 |
| Title |
Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods for RNA-Seq of low quality and/or low quantity samples, but their relative merits have not been systematically analyzed. Here, we compare five such methods using a comprehensive set of metrics, relevant to applications such as transcriptome annotation, transcript discovery, and gene expression. Using a single human RNA sample, we constructed and deeply sequenced 10 libraries with these methods and two control libraries. We find that the RNase H method performed best for low quality RNA, and can even effectively replace oligo (dT) based methods for standard RNA-Seq. SMART and NuGEN had distinct strengths for low quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development.
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| |
|
| Overall design |
Examination of 9 different RNA-Seq libraries starting from total RNA from 5 distinct methods; also 3 control RNA-Seq libraries
|
| |
|
| Contributor(s) |
Levin JZ, Regev A, Adiconis X |
| Citation(s) |
23685885 |
| Submission date |
Sep 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Joshua Z Levin |
| Organization name |
Broad Institute of MIT & Harvard
|
| Street address |
320 Charles Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02141 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (18)
|
|
| Relations |
| BioProject |
PRJNA174728 |
| SRA |
SRP015640 |
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