TY - JOUR
T1 - Challenges and considerations for reproducibility of STARR-seq assays
AU - Das, Maitreya
AU - Hossain, Ayaan
AU - Banerjee, Deepro
AU - Praul, Craig Alan
AU - Girirajan, Santhosh
N1 - Publisher Copyright:
© 2023 Cold Spring Harbor Laboratory Press. All rights reserved.
PY - 2023/4
Y1 - 2023/4
N2 - High-throughput methods such as RNA-seq, ChIP-seq, and ATAC-seq have well-established guidelines, commercial kits, and analysis pipelines that enable consistency and wider adoption for understanding genome function and regulation. STARR-seq, a popular assay for directly quantifying the activities of thousands of enhancer sequences simultaneously, has seen limited standardization across studies. The assay is long, with more than 250 steps, and frequent customization of the protocol and variations in bioinformatics methods raise concerns for reproducibility of STARR-seq studies. Here, we assess each step of the protocol and analysis pipelines from published sources and in-house assays, and identify critical steps and quality control (QC) checkpoints necessary for reproducibility of the assay. We also provide guidelines for experimental design, protocol scaling, customization, and analysis pipelines for better adoption of the assay. These resources will allow better optimization of STARR-seq for specific research needs, enable comparisons and integration across studies, and improve the reproducibility of results.
AB - High-throughput methods such as RNA-seq, ChIP-seq, and ATAC-seq have well-established guidelines, commercial kits, and analysis pipelines that enable consistency and wider adoption for understanding genome function and regulation. STARR-seq, a popular assay for directly quantifying the activities of thousands of enhancer sequences simultaneously, has seen limited standardization across studies. The assay is long, with more than 250 steps, and frequent customization of the protocol and variations in bioinformatics methods raise concerns for reproducibility of STARR-seq studies. Here, we assess each step of the protocol and analysis pipelines from published sources and in-house assays, and identify critical steps and quality control (QC) checkpoints necessary for reproducibility of the assay. We also provide guidelines for experimental design, protocol scaling, customization, and analysis pipelines for better adoption of the assay. These resources will allow better optimization of STARR-seq for specific research needs, enable comparisons and integration across studies, and improve the reproducibility of results.
UR - http://www.scopus.com/inward/record.url?scp=85159735694&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85159735694&partnerID=8YFLogxK
U2 - 10.1101/gr.277204.122
DO - 10.1101/gr.277204.122
M3 - Article
C2 - 37130797
AN - SCOPUS:85159735694
SN - 1088-9051
VL - 33
SP - 479
EP - 495
JO - Genome research
JF - Genome research
IS - 4
ER -