|
| Status |
Public on Mar 21, 2018 |
| Title |
Comprehensive comparative analysis of 5’ end RNA sequencing methods |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
RNA-Seq is an effective method to study the transcriptome, but specialized methods are required to identify 5’ ends of transcripts. Several published strategies exist for this specific purpose, but their relative merits have not been systematically analyzed. Here, we directly compare the performance of six such methods – testing five with cellular RNA as well as a novel spike-in RNA assay that helps address interpretation challenges that arise from uncertainties in annotation or RNA processing. Using a single human RNA sample, we constructed and sequenced 18 libraries with these methods and one standard, control RNA-Seq library. We find that the CAGE method performed best for mRNA and that most of its unannotated peaks are supported by evidence from other genomic methods. We then applied CAGE to eight brain-related samples and revealed sample-specific transcription start site (TSS) usage as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.
|
| |
|
| Overall design |
Examination of 19 different RNA-Seq libraries starting from total RNA from 5 distinct 5' end methods; also 1 control RNA-Seq library
|
| |
|
| Contributor(s) |
Levin JZ, Adiconis X, Haber A, Simmons SK |
| Citation(s) |
29867192 |
| Submission date |
Sep 05, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Joshua Levin |
| E-mail(s) |
jlevin@broadinstitute.org
|
| Organization name |
Broad Institute
|
| Department |
Stanley Center
|
| Street address |
75 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (19)
|
|
| Relations |
| BioProject |
PRJNA401781 |
| SRA |
SRP116908 |
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