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SRX1325673: GSM1905646: Xla_J_strain_NF12_RiboZero; Xenopus laevis; RNA-Seq
1 ILLUMINA (Illumina HiSeq 1000) run: 50.3M spots, 10.2G bases, 6Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero]
show Abstracthide Abstract
A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs expressed over time during embryogenesis. Here we present a comprehensive characterization of protein and mRNA dynamics across early development in Xenopus. Surprisingly, we find that most proteins change very little and duplicated genes are expressed similarly. While the correlation between mRNA levels and protein expression is poor, a mass action kinetics model parametrized by the protein synthesis and degradation rates regresses protein dynamics to RNA dynamics, corrected for initial protein concentration. This study provides a rich resource for developmental biologists, unveiling detailed data for absolute levels of ~10K proteins and ~28K transcripts via convenient web portal. It underscores the lasting impact of maternal dowry, finds surprisingly few cases where degradation alone drives a change in protein level, and highlights the importance of transcription in shaping the proteome. Overall design: mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification.
Sample: Xla_J_strain_NF12_RiboZero
SAMN04158983 • SRS1110729 • All experiments • All runs
Organism: Xenopus laevis
Library:
Instrument: Illumina HiSeq 1000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: total RNA was extracted using TRIzol and phase-lock tubes libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification
Experiment attributes:
GEO Accession: GSM1905646
Links:
Runs: 1 run, 50.3M spots, 10.2G bases, 6Gb
Run# of Spots# of BasesSizePublished
SRR261410850,268,50910.2G6Gb2015-11-06

ID:
1890793

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