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Series GSE141851 Query DataSets for GSE141851
Status Public on Jul 21, 2020
Title Massively parallel and time-resolved RNA sequencing in single cells with scNT-Seq
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Single-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal RNA dynamics. Here we present single-cell metabolically labeled new RNA tagging sequencing (scNT-Seq), a method for massively parallel analysis of newly-transcribed and pre-existing mRNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads, efficiently marking newly-transcribed mRNAs with T-to-C substitutions. With scNT-Seq, we jointly profiled new and old transcriptomes in ~55,000 single cells. These data revealed time-resolved transcription factor activities and cell state trajectories at single-cell level in response to neuronal activation. We further determined rates of RNA biogenesis and decay to uncover RNA regulatory strategies during stepwise conversion between pluripotent and rare totipotent two-cell-embryo-like (2C-like) stem cell states. Finally, integrating scNT-Seq with genetic perturbation identifies DNA methylcytosine dioxygenases as an epigenetic barrier into 2C-like cell state. Time-resolved single-cell transcriptomic analysis thus opens new lines of inquiry regarding cell-type-specific RNA regulatory mechanisms.
Overall design Single-cell metabolically labeled new RNA tagging sequencing
Contributor(s) Qiu Q, Hu P, Qiu X, Govek K, Gonzalez-Camara P, Wu H
Citation(s) 32868927
Submission date Dec 11, 2019
Last update date Sep 26, 2020
Contact name Peng Hu
Organization name University of Pennsylvanian
Department Genetics
Lab Hao Wu
Street address 415 Curie Blvd, 545 CRB
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (38)
GSM4214720 Mix-4sU
GSM4214721 Mix-4sU-TFEA
GSM4214722 Mix-4sU-IAA
BioProject PRJNA594978
SRA SRP236894

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE141851_RAW.tar 164.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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