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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Fishman, Lior; Modak, Avani; Nechooshtan, Gal; Razin, Tayla; +4 Authors

    During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We then introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell-types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response. This repository contains the raw microscopy data that is analyzed in Figures 6F-I and Supplementary Figure S4 B-D.

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    Authors: Harnik, Yotam; Yakubovsky, Oran; Hoefflin, Rouven; Itzkovitz, Shalev;

    QuPath project containing all highly-multiplex images generated with the PhenoCycler Fusion platform from the publication “A spatial expression atlas of the adult human proximal small intestine” including nuclear segmentation masks and cell annotations. Whole slide scans of staining with Hyaluronic-Acid binding protein and H&E staining of the same sections are provided. Moreover, the following matrices needed to reproduce the main results are provided: "cells.csv": cells table including centroid coordinates and annotations "raw_mat.csv": protein expression matrix without pre-processing "norm_mat.csv": protein expression matrix after log2-transformation and per sample z-scoring

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    A collection of all plots generated for deriving the conclusions seen in "A comparison of model-based and model-free agents in solving semi-automatically generated PPDDL problems".

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    SEM images of bryozoan samples from the historical collections of the Hebrew University, scenned as part of a virtual access Synthesys project

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    SEM images of bryozoan samples from the historical collections of the Hebrew University, scenned as part of a virtual access Synthesys project

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    Authors: Charidemou, Evelina; Tsiarli, Maria A.; Theophanous, Andria; Yilmaz, Vural; +4 Authors

    Additional file 5: Figure S5. Validation of NAA40 knock-down in L3 larvae fat bodies. RT-qPCR analysis of Naa40 in control and NAA40-KD FBs (n = 3/group; 4-5 larvae FB in each biological repeat). Data are presented as mean �� SEM and analysed by unpaired 2-tailed student���s t-test; *P ��� 0.05, ** P ��� 0.01, *** P ��� 0.001. Individual values can be found in Additional file 9: Table S11.

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    Authors: Charidemou, Evelina; Tsiarli, Maria A.; Theophanous, Andria; Yilmaz, Vural; +4 Authors

    Additional file 4: Figure S4. Histone deacetylation-derived acetate is an important source for lipid accumulation upon NAA40 depletion. (A) Schematic representation of the different routes for the synthesis of acetyl-CoA in mammalian cells. (B) Representative immunoblot run in triplicate using antibodies against the indicated histone acetylation marks in scramble and NA40-KD cells with and without sodium butyrate, 48 h after siRNA treatment (n = 3/group). (C) Visualisation (left) and quantification (right) of lipid droplets by Nile red (red) and nuclei by DAPI (blue) in scramble and NAA40-KD cells with and without sodium butyrate, 48 h after siRNA treatment; Scale bar = 25 ��m (n = 6-10/group). (D) RT-qPCR analysis of expression of Naa40, Acly and Acss2 mRNA levels in scramble and NAA40-KD, ACSS22-KD and NAA40-KD + ACSS2-KD cells after 48 h of siRNA treatment (n = 3/group). (E) Visualisation (left) and quantification (right) of lipid droplets by Nile red (red) and nuclei by DAPI (blue) in NAA40-KD, ACSS22-KD and NAA40-KD + ACSS2-KD cells after 48 h of siRNA treatment; Scale bar = 25 ��m (n = 6-8/group). Data are presented as mean �� SEM and analysed by 1-way ANOVA with post hoc Dunnett���s multiple-comparisons test; *P ��� 0.05, ** P ��� 0.01, *** P ��� 0.001. Individual values can be found in Additional file 9: Table S10.

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    Authors: Charidemou, Evelina; Tsiarli, Maria A.; Theophanous, Andria; Yilmaz, Vural; +4 Authors

    Additional file 3: Figure S3. AML12 hepatocytes are in an anabolic state upon NAA40 depletion. Normalised intensity of NAD+, NADH, NADH/NAD+ and ATP measured by LC-MS in scramble and Naa40-KD cells after 48 h of siRNA treatment (n = 4/group). Data are presented as mean �� SEM and analysed by unpaired 2-tailed student���s t-test; *P ��� 0.05, ** P ��� 0.01, *** P ��� 0.001. Individual values can be found in Additional file 9: Table S9.

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    Authors: Charidemou, Evelina; Tsiarli, Maria A.; Theophanous, Andria; Yilmaz, Vural; +4 Authors

    Additional file 1: Figure S1. NAA40 is readily expressed in human liver amongst different transcriptomic and proteomic studies. Data were extracted from Human Expression Atlas of EMBL-EBI and were filtered to select only the high expression levels of NAA40 in RNA-sequencing and proteomic experiments. Each dot corresponds to the presence of NAA40, while where there is no dot, they are no available data.

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    Authors: Fishman, Lior; Modak, Avani; Nechooshtan, Gal; Razin, Tayla; +4 Authors

    During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We then introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell-types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response. This repository contains the raw microscopy data that is analyzed in Figures 6F-I and Supplementary Figure S4 B-D.

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    Authors: Harnik, Yotam; Yakubovsky, Oran; Hoefflin, Rouven; Itzkovitz, Shalev;

    QuPath project containing all highly-multiplex images generated with the PhenoCycler Fusion platform from the publication “A spatial expression atlas of the adult human proximal small intestine” including nuclear segmentation masks and cell annotations. Whole slide scans of staining with Hyaluronic-Acid binding protein and H&E staining of the same sections are provided. Moreover, the following matrices needed to reproduce the main results are provided: "cells.csv": cells table including centroid coordinates and annotations "raw_mat.csv": protein expression matrix without pre-processing "norm_mat.csv": protein expression matrix after log2-transformation and per sample z-scoring

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    A collection of all plots generated for deriving the conclusions seen in "A comparison of model-based and model-free agents in solving semi-automatically generated PPDDL problems".

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    SEM images of bryozoan samples from the historical collections of the Hebrew University, scenned as part of a virtual access Synthesys project

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    License: CC BY
    Data sources: ZENODO
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    Data sources: Datacite
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