Limits...
Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.

Smits AH, Lindeboom RG, Perino M, van Heeringen SJ, Veenstra GJ, Vermeulen M - Nucleic Acids Res. (2014)

Bottom Line: While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies.Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance.Comparison between the single-cell proteome and transcriptome reveal poor expression correlation.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands Cancer Genomics Netherlands, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands.

Show MeSH

Related in: MedlinePlus

Dynamics of proteome and transcriptome in early Xenopus embryogenesis. (A) Schematic depiction of the workflow (upper panel) and the calculated protein content of X. leavis egg and embryo 10.5 (lower panel). (B) Unsupervised correlation-based clustering of egg and embryo 10.5 proteomes clearly separates egg and embryo 10.5 proteomes. (C) Heatmap of significant regulated proteins between egg and embryo 10.5, identified by an adapted t-test (FDR = 0.005 and s0 = 1). (D) Enriched GO terms for both egg and embryo 10.5 enriched proteins, as identified in C. Y-axis represents the –log FDR. (E) Protein and mRNA ratios (egg/embryo 10.5) for both egg (left panel) and embryo 10.5 (right panel) enriched proteins reveal lack of correlation between protein and mRNA dynamics. See also Supplementary Table S4.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4150773&req=5

Figure 4: Dynamics of proteome and transcriptome in early Xenopus embryogenesis. (A) Schematic depiction of the workflow (upper panel) and the calculated protein content of X. leavis egg and embryo 10.5 (lower panel). (B) Unsupervised correlation-based clustering of egg and embryo 10.5 proteomes clearly separates egg and embryo 10.5 proteomes. (C) Heatmap of significant regulated proteins between egg and embryo 10.5, identified by an adapted t-test (FDR = 0.005 and s0 = 1). (D) Enriched GO terms for both egg and embryo 10.5 enriched proteins, as identified in C. Y-axis represents the –log FDR. (E) Protein and mRNA ratios (egg/embryo 10.5) for both egg (left panel) and embryo 10.5 (right panel) enriched proteins reveal lack of correlation between protein and mRNA dynamics. See also Supplementary Table S4.

Mentions: The RNA-Seq experiments resulted in 42 bp single-end sequences that were mapped to the X. laevis genome (JGI 7.1) using gmap (26), allowing one mismatch and were stored in BAM files. BamTools API 1.0.2 (27) was used to sort and index the reads. Transcript abundance was calculated by quantifying the Reads Per Kilobase of transcript per Million reads mapped (RPKM value) using Cufflinks v2.1.1 (28). To compare the transcriptomes of the X. laevis eggs and embryos 10.5 with high confidence (Figure 4C and Supplementary Figure S3A), the RNA-Seq profiles were merged for each developmental stage using the BamTools API, followed by the removal of random sequences with SAMtools v0.1.18 (29) until the amount of mapped reads were similar.


Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.

Smits AH, Lindeboom RG, Perino M, van Heeringen SJ, Veenstra GJ, Vermeulen M - Nucleic Acids Res. (2014)

Dynamics of proteome and transcriptome in early Xenopus embryogenesis. (A) Schematic depiction of the workflow (upper panel) and the calculated protein content of X. leavis egg and embryo 10.5 (lower panel). (B) Unsupervised correlation-based clustering of egg and embryo 10.5 proteomes clearly separates egg and embryo 10.5 proteomes. (C) Heatmap of significant regulated proteins between egg and embryo 10.5, identified by an adapted t-test (FDR = 0.005 and s0 = 1). (D) Enriched GO terms for both egg and embryo 10.5 enriched proteins, as identified in C. Y-axis represents the –log FDR. (E) Protein and mRNA ratios (egg/embryo 10.5) for both egg (left panel) and embryo 10.5 (right panel) enriched proteins reveal lack of correlation between protein and mRNA dynamics. See also Supplementary Table S4.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150773&req=5

Figure 4: Dynamics of proteome and transcriptome in early Xenopus embryogenesis. (A) Schematic depiction of the workflow (upper panel) and the calculated protein content of X. leavis egg and embryo 10.5 (lower panel). (B) Unsupervised correlation-based clustering of egg and embryo 10.5 proteomes clearly separates egg and embryo 10.5 proteomes. (C) Heatmap of significant regulated proteins between egg and embryo 10.5, identified by an adapted t-test (FDR = 0.005 and s0 = 1). (D) Enriched GO terms for both egg and embryo 10.5 enriched proteins, as identified in C. Y-axis represents the –log FDR. (E) Protein and mRNA ratios (egg/embryo 10.5) for both egg (left panel) and embryo 10.5 (right panel) enriched proteins reveal lack of correlation between protein and mRNA dynamics. See also Supplementary Table S4.
Mentions: The RNA-Seq experiments resulted in 42 bp single-end sequences that were mapped to the X. laevis genome (JGI 7.1) using gmap (26), allowing one mismatch and were stored in BAM files. BamTools API 1.0.2 (27) was used to sort and index the reads. Transcript abundance was calculated by quantifying the Reads Per Kilobase of transcript per Million reads mapped (RPKM value) using Cufflinks v2.1.1 (28). To compare the transcriptomes of the X. laevis eggs and embryos 10.5 with high confidence (Figure 4C and Supplementary Figure S3A), the RNA-Seq profiles were merged for each developmental stage using the BamTools API, followed by the removal of random sequences with SAMtools v0.1.18 (29) until the amount of mapped reads were similar.

Bottom Line: While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies.Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance.Comparison between the single-cell proteome and transcriptome reveal poor expression correlation.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands Cancer Genomics Netherlands, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands.

Show MeSH
Related in: MedlinePlus