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SciMET-cap: High-throughput single-cell methylation analysis with a reduced sequencing burden

ABSTRACT: sciMET-cap: High-throughput single-cell methylation analysis with a reduced sequencing burden

PROVIDER: PRJNA1053297 | ENA |

REPOSITORIES: ENA

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sciMET-cap: High-throughput single-cell methylation analysis with a reduced sequencing burden

Project description:DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are now possible (sciMET); however, the genome-wide nature of DNA methylation results in a high sequencing burden per cell. Here, we leverage target enrichment with sciMET to capture sufficient information per cell for cell type assignment using substantially fewer sequence reads (sciMET-cap). Sufficient off-target coverage further enables the production of near-complete methylomes for individual cell types. We characterize sciMET-cap on human PBMCs and brain (middle frontal gyrus).

2023-12-19 | GSE250282 | GEO

mRNA cap methylation in pluripotency and differentiation

Project description:The mRNA cap recruits factors essential for transcript processing and translation initiation. We report that regulated mRNA cap methylation is a feature of embryonic stem cell (ESC) differentiation. Expression of the mRNA cap methyltransferase activating subunit, RAM, is elevated in ESCs resulting in high levels of mRNA cap methylation and expression of Oct4 and Sox2 and other pluripotency-associated factors. During neural differentiation, RAM is suppressed which is required for loss of Oct4 and Sox2 and correct expression of neural markers. Cells were treated with control or RAM siRNA and cytosolic RNA or polysome RNA (actively translated) was sequenced.

2016-06-14 | E-GEOD-81849 | biostudies-arrayexpress

mRNA cap methylation in pluripotency and differentiation

2016-06-14 | GSE81849 | GEO

HDR-CRISPR promotes targeted genome editing with reduced mutational burden in primary human cells

Project description:HDR-CRISPR promotes targeted genome editing with reduced mutational burden in primary human cells

| PRJNA935715 | ENA

Systematic discovery of cap-independent translation sequences in human and viral genomesÂ

Project description:To investigate gene specificity at the level of translation in both the human genome and viruses we devised a high-throughput bicistronic assay to quantify cap-independent translation. We uncover thousands of novel cap-independent translation sequences and provide insights on the landscape of translational regulation in both human and viruses. We find extensive translational elements in the 3â untranslated region (3âUTR) of human transcripts and the polyprotein region of un-capped RNA viruses. Through the characterization of regulatory elements underlying cap-independent translation activity we identify potential mechanisms of secondary structure, short sequence motif and base-pairing with the 18S rRNA. Furthermore, we systematically map the 18S rRNA regions for which reverse complementary enhance translation. Thus we provide insights into the mechanisms of translational control in humans and viruses. high-throughput bicistronic assay for obtaining cap-independent translation measurements of 55,000 fully designed sequences in parallel using fluorescence-activated cell sorting and high-throughput DNA sequencing (FACS-seq).

2015-10-23 | E-GEOD-74277 | biostudies-arrayexpress

HDR-CRISPR promotes targeted genome editing with reduced mutational burden in primary human cells [Amp-seq]

Project description:HDR-CRISPR promotes targeted genome editing with reduced mutational burden in primary human cells [Amp-seq]

| PRJNA935730 | ENA

HDR-CRISPR promotes targeted genome editing with reduced mutational burden in primary human cells [CAST-seq]

Project description:HDR-CRISPR promotes targeted genome editing with reduced mutational burden in primary human cells [CAST-seq]

| PRJNA935729 | ENA

LCL Bio-CAP-seq

Project description:LCL Bio-CAP-seq

| PRJNA795784 | ENA

Human senescence PRO-cap

Project description:Human senescence PRO-cap

| PRJNA658592 | ENA

Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution

Project description:We introduce Chemical-crosslinking Assisted Proximity Capture (CAP-C), a method that utilizes multi-functional chemical crosslinkers with defined physical sizes to directly assess spatial distances between nuclear genomic sequences. CAP-C avoids limitations caused by extensive protein-DNA crosslinking in most in situ methods, and thus generates chromatin contact maps at high resolution with low background noise.

2020-08-22 | GSE110061 | GEO

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