Ozadam et al. 2023 (PRJNA770650)

General Details

Title Single cell quantification of ribosome occupancy in early mouse development
Organism
Number of Samples 61
Release Date 2021/10/12 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP341033
ENA SRP341033
GEO
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 Ribo-Seq
SRR16299900 PRJNA770650 Mus musculus Ribo-Seq
SRR16299923 PRJNA770650 Mus musculus Ribo-Seq
SRR16299924 PRJNA770650 Mus musculus Ribo-Seq
SRR16299925 PRJNA770650 Mus musculus Ribo-Seq
SRR16299926 PRJNA770650 Mus musculus Ribo-Seq
SRR16299927 PRJNA770650 Mus musculus Ribo-Seq
SRR16299928 PRJNA770650 Mus musculus Ribo-Seq
SRR16299929 PRJNA770650 Mus musculus Ribo-Seq
SRR16299930 PRJNA770650 Mus musculus Ribo-Seq
SRR16299931 PRJNA770650 Mus musculus Ribo-Seq
SRR16299932 PRJNA770650 Mus musculus Ribo-Seq
SRR16299933 PRJNA770650 Mus musculus Ribo-Seq
SRR16299934 PRJNA770650 Mus musculus Ribo-Seq
SRR16299883 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299884 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299885 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299886 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299887 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299888 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299889 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299890 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299891 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299892 PRJNA770650 Mus musculus Ribo-Seq
SRR16299893 PRJNA770650 Mus musculus Ribo-Seq
SRR16299894 PRJNA770650 Mus musculus Ribo-Seq
SRR16299895 PRJNA770650 Mus musculus Ribo-Seq
SRR16299896 PRJNA770650 Mus musculus Ribo-Seq
SRR16299897 PRJNA770650 Mus musculus Ribo-Seq
SRR16299898 PRJNA770650 Mus musculus Ribo-Seq
SRR16299901 PRJNA770650 Mus musculus Ribo-Seq
SRR16299902 PRJNA770650 Mus musculus Ribo-Seq
SRR16299903 PRJNA770650 Mus musculus Ribo-Seq
SRR16299904 PRJNA770650 Mus musculus Ribo-Seq
SRR16299905 PRJNA770650 Mus musculus Ribo-Seq
SRR16299906 PRJNA770650 Mus musculus K562 Ribo-Seq
SRR16299907 PRJNA770650 Mus musculus Ribo-Seq
SRR16299908 PRJNA770650 Mus musculus Ribo-Seq
SRR16299909 PRJNA770650 Mus musculus Ribo-Seq
SRR16299910 PRJNA770650 Mus musculus Ribo-Seq
SRR16299911 PRJNA770650 Mus musculus Ribo-Seq
SRR16299912 PRJNA770650 Mus musculus Ribo-Seq
SRR16299913 PRJNA770650 Mus musculus Ribo-Seq
SRR16299914 PRJNA770650 Mus musculus Ribo-Seq
SRR16299915 PRJNA770650 Mus musculus Ribo-Seq
SRR16299916 PRJNA770650 Mus musculus Ribo-Seq
SRR16299917 PRJNA770650 Mus musculus Ribo-Seq
SRR16299918 PRJNA770650 Mus musculus Ribo-Seq
SRR16299919 PRJNA770650 Mus musculus Ribo-Seq
SRR16299920 PRJNA770650 Mus musculus Ribo-Seq
SRR16299921 PRJNA770650 Mus musculus Ribo-Seq
SRR16299922 PRJNA770650 Mus musculus Ribo-Seq
SRR24205223 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR24205224 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR24205225 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR24205226 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR24205227 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR24205228 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR24205229 PRJNA770650 Homo sapiens K562 Ribo-Seq
SRR16299955 PRJNA770650 Mus musculus K562 RNA-Seq
SRR16299956 PRJNA770650 Mus musculus K562 RNA-Seq
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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