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LaminB1 DamID analysis in RIF1 depleted preimplantation mouse embryos

ABSTRACT: LaminB1 DamID analysis in RIF1 depleted preimplantation mouse embryos

PROVIDER: PRJNA1093387 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR28496600.fastq.gz	Fastqsanger.gz
	SRR28496601.fastq.gz	Fastqsanger.gz
	SRR28496602.fastq.gz	Fastqsanger.gz
	SRR28496603.fastq.gz	Fastqsanger.gz
	SRR28496592.fastq.gz	Fastqsanger.gz

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LaminB1 DamID analysis in RIF1 depleted preimplantation mouse embryos

Project description:We investigated how RIF1 depletion affects the nuclear organization in mouse preimplantation embryos by performing DamID-seq to map lamina-associated domains (LADs).

2025-03-18 | GSE262788 | GEO

LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos

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Single embryo RNA-seq analysis in RIF1 depleted preimplantation mouse embryos

Project description:RNAseq datasets from control and RIF1-depleted mouse embryos to address whether RIF1 depletion results in changes in gene expression. siRNA was microinjected at the zygote stage and controls (embryos injected with siRNA control) and RIF1-depleted embryos (embryos injected with siRNA against Rif1) were collected either at the 4-cell or at the 8-cell stage. RNAseq was performed using SMART-Seq2 in single embryos.

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Single embryo RNA-seq analysis in RIF1 depleted preimplantation mouse embryos

Project description:Single embryo RNA-seq analysis in RIF1 depleted preimplantation mouse embryos

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Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos

Project description:Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos

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DamID LaminB1 data in mouse MEFs, wild-type and POU2F1-/-. DamID LaminA data in mouse Neural Precursor Cells and Astrocytes.

Project description:DamID LaminB1 data were generated in POU2F1-/- MEFs to study the potential role of POU2F1/Oct1 in genome - nuclear lamina interactions. DamID LaminA data were generated in NPCs and Astrocytes to study similarities/differences between LaminA and LaminB1 binding. The procedure to arrive at the provided Hidden Markov Model (HMM) state calls is as follows: We fitted a two-state HMM whereby emissions are distributed as Student's t variables. Mean and variance of DamID signals differ between states, but the degree of freedom (nu) is the same. Gaps in the probe coverage were filled by evenly spaced null probe-values. The parameters were estimated by an adaptation of the ECME algorithm to the HMM framework, showing faster convergence than regular EM when nu is unknown (Filion et al., Cell, 2010). State calls were derived through the Viterbi algorithm. This process was repeated separately for each cell type, yielding per-probe calls. Probes in the ‘bound’ (1) state are indicated as LAD-probes, probes in the ‘unbound’ (0) state as inter-LAD-probes.

2012-10-10 | GSE36132 | GEO

Gene expression of Rif1-depleted ES cells

Project description:Gene expression of Rif1-depleted ES cells

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LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-03-18 | GSE262791 | GEO

Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos

Project description:Repli-seq datasets were generated using single cell Repli-seq as described in Nakatani et al. (2024). Embryos were microinjected with an siRNA control or an siRNA against Rif1 at the zygote stage. Individual cells were collected for scRepli-seq at the 4-cell, 8-cell and Morula stage embryos.

2025-03-18 | GSE262790 | GEO

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