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SLIC-CAGE (Super-Low Input Carrier-CAGE) transcription start site mapping of mouse migratory and gonadal primordial germ cells, postnatal oocytes and early embryo

ABSTRACT: SLIC-CAGE (Super-Low Input Carrier-CAGE) transcription start site mapping of mouse migratory and gonadal primordial germ cells, postnatal oocytes and early embryo

PROVIDER: PRJEB41307 | ENA |

REPOSITORIES: ENA

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SLIC-CAGE (Super-Low Input Carrier-CAGE) development: comparison with Saccharomyces cerevisiae nAnTi-CAGE and nanoCAGE libraries and validation of SLIC-CAGE on Mus musculus total RNA

Project description:We developed SLIC-CAGE (Super-Low Input Carrier-CAGE) approach to capture 5'end of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. The dramatic increase in sensitivity compared to existing CAGE methods is achieved by specially designed, selectively degradable carrier RNA. We tested SLIC-CAGE on Saccharomyces cerevisiae (BY4741 strain) and produced libraries from 1-100 ng of total cellular RNA. We also produced S. cerevisiae nAnT-iCAGE libraries as the current gold-standard CAGE libraries using the recommended 5 micrograms of total cellular RNA to assess the quality of SLIC-CAGE libraries produces with up to 1000-fold less material. We provide a direct comparison between SLIC-CAGE and the latest nanoCAGE protocol (libraries created using S. cerevisiae total RNA) and show that SLIC-CAGE produces unbiased libraries of higher complexity and quality than nanoCAGE. Finally, we provide SLIC-CAGE libraries on mouse embryonic stem cells (E14) using 5-100 ng of total cellular RNA as starting material.

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SLIC-CAGE (Super-Low Input Carrier-CAGE) transcription start site mapping of mouse migratory and gonadal primordial germ cells, postnatal oocytes and early embryo

Project description:We used SLIC-CAGE to map transcription start sites (TSSs) of mouse primordial germ cells from embryonic days 9.5-16.5, postnatal oocytes (P6, P14 and MII), and early 2-cell and 4-cell mouse embryos. We use this TSS data to show that the mouse germline development starts with the somatic promoter code with a prominent switch to the maternal code (W-box dependent) occurring during the follicular oogenesis. We also find that the promoters of gonadal germ cells are characterised by a previously unknown divergence from the somatic transcription initiation. This divergence is distinct from the promoter code used later by the developing oocytes and reveals genome-wide promoter remodelling during early female and male germline development.

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SLIC-CAGE (Super-Low Input Carrier-CAGE) development: comparison with Saccharomyces cerevisiae nAnTi-CAGE and nanoCAGE libraries and validation of SLIC-CAGE on Mus musculus total RNA

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SLIC-CAGE (Super-Low Input Carrier-CAGE) application on mouse primordial germ cells isolated from embryonic day E11.5

Project description:SLIC-CAGE (Super-Low Input Carrier-CAGE) application on mouse primordial germ cells isolated from embryonic day E11.5

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Nuclear SLIC-CAGE of human cortical neurons from Cornelia de Lange Syndrome patients and control individuals

Project description:We used SLIC-CAGE to map transcriptional start sites in cortical neurons from Cornelia de Lange Syndrome (CdLS) patients and control individuals. SLIC-CAGE was performed using nuclear RNA isolated from pre-frontal cortical grey matter. Usage of nuclear RNA allows enrichment of unstable RNAs, such as RNA originating from enhancer transcription. We characterised promoter-level gene expression in cortical neurons from CdLS patients and found deregulation of hundreds of genes enriched for neuronal functions.

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2020-10-01 | GSE151473 | GEO

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