Ozadam et al. 2023 (PRJNA770650)

General Details

Title Single cell quantification of ribosome occupancy in early mouse development
Organism
Number of Samples 59
Release Date 2021/10/12 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP341033
ENA SRP341033
GEO GSE185732
BioProject PRJNA770650

Publication

Title
Authors Ozadam H, Tonn T, Han CM, Segura A, Hoskins I, Rao S, Ghatpande V, Tran D, Catoe D, Salit M, Cenik C
Journal Nature
Publication Date 2023 Jun
Abstract Translation regulation is critical for early mammalian embryonic development 1 . However, previous studies had been restricted to bulk measurements 2 , precluding precise determination of translation regulation including allele-specific analyses. Here, to address this challenge, we developed a novel microfluidic isotachophoresis (ITP) approach, named RIBOsome profiling via ITP (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N 6 -methyladenosine modification of RNAs. Our high-coverage measurements enabled, to our knowledge, the first analysis of allele-specific ribosome engagement in early development. These led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allele-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle-stage oocytes is the predominant determinant of protein abundance in the zygote. The Ribo-ITP approach will enable numerous applications by providing high-coverage and high-resolution ribosome occupancy measurements from ultra-low input samples including single cells. © 2023. The Author(s).
PMC PMC10307641
PMID 37344592
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR16299899 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299900 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299923 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299924 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299925 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299926 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299927 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299928 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299929 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299930 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299931 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299932 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299933 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299934 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299883 PRJNA770650 Homo sapiens K562 Ribo-Seq Frozen
SRR16299884 PRJNA770650 Homo sapiens K562 Ribo-Seq Frozen
SRR16299885 PRJNA770650 Homo sapiens K562 Ribo-Seq Frozen
SRR16299886 PRJNA770650 Homo sapiens K562 Ribo-Seq Frozen
SRR16299887 PRJNA770650 Homo sapiens K562 Ribo-Seq Frozen
SRR16299888 PRJNA770650 Homo sapiens K562 Ribo-Seq Frozen
SRR16299889 PRJNA770650 Homo sapiens K562 Ribo-Seq Frozen
SRR16299890 PRJNA770650 Homo sapiens K562 Ribo-Seq Frozen
SRR16299891 PRJNA770650 Homo sapiens K562 Ribo-Seq Frozen
SRR16299892 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299893 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299894 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299895 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299896 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299897 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299898 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299901 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299902 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299903 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299904 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299905 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299906 PRJNA770650 Mus musculus K562 Ribo-Seq Frozen
SRR16299907 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299908 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299909 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299910 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299911 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299912 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299913 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299914 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299915 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299916 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299917 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299918 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299919 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299920 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299921 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR16299922 PRJNA770650 Mus musculus 0.0 Ribo-Seq Frozen
SRR24205223 PRJNA770650 Homo sapiens K562 Ribo-Seq 0.0
SRR24205224 PRJNA770650 Homo sapiens K562 Ribo-Seq 0.0
SRR24205225 PRJNA770650 Homo sapiens K562 Ribo-Seq 0.0
SRR24205226 PRJNA770650 Homo sapiens K562 Ribo-Seq 0.0
SRR24205227 PRJNA770650 Homo sapiens K562 Ribo-Seq 0.0
SRR24205228 PRJNA770650 Homo sapiens K562 Ribo-Seq 0.0
SRR24205229 PRJNA770650 Homo sapiens K562 Ribo-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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