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Series GSE189482 Query DataSets for GSE189482
Status Public on Jan 08, 2022
Title Precise Transcript Reconstruction with End-Guided Assembly
Organism Arabidopsis thaliana
Experiment type Other
Summary Accurate annotation of transcript isoforms is crucial to understand gene functions, but automated methods for reconstructing full-length transcripts from RNA sequencing (RNA-seq) data remain imprecise. We developed Bookend, a software package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. Through end-guided assembly with Bookend we demonstrate that correct modeling of transcript start and end sites is essential for precise transcript assembly. Furthermore, we discovered that utilization of end-labeled reads present in full-length single-cell RNA-seq (scRNA-seq) datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells (mESCs) can produce end-to-end transcript annotations of comparable quality to reference annotations in these model organisms.
Overall design Two PacBio Iso-seq libraries were generated each using 10 µg of total RNA from Arabidopsis inflorescences containing unopened floral buds. Total RNA was extracted with TRIzol following the method described in (Schon et al. 2018. Genome Research) to yield two biological replicates with an RNA integrity number (RIN) of 9.0 and 9.2, respectively. SMRTbell libraries were constructed by the Vienna BioCenter Core Facilities (VBCF) and sequenced on a Sequel SMRT Cell 1M.
Contributor(s) Nodine M, Schon M
Citation(s) 35768836
Submission date Nov 24, 2021
Last update date Jul 07, 2022
Contact name Michael D Nodine
Organization name Wageningen University & Research
Department Plant Sciences
Lab Molecular Biology
Street address Radix West
City Wageningen
State/province Gelderland
ZIP/Postal code 6708 PB
Country Netherlands
Platforms (1)
GPL25661 Sequel (Arabidopsis thaliana)
Samples (2)
GSM5702444 Col-0 floral bud PacBio (biorep #1)
GSM5702445 Col-0 floral bud PacBio (biorep #2)
BioProject PRJNA783213
SRA SRP347597

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Supplementary file Size Download File type/resource
GSE189482_RAW.tar 9.2 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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