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Homo sapiens

ABSTRACT: Genome-wide maps of nuclear lamina interactions in single human cells. (DamID LaminB1, clone-5-8, haploid)

PROVIDER: PRJNA282148 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1995800.fastq.gz	Fastqsanger.gz
	SRR1995810.fastq.gz	Fastqsanger.gz
	SRR1995791.fastq.gz	Fastqsanger.gz
	SRR1995801.fastq.gz	Fastqsanger.gz
	SRR1995811.fastq.gz	Fastqsanger.gz

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Project description:Genome-wide maps of nuclear lamina interactions in single human cells. (DamID LaminB1, clone-14, haploid)

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Project description:Genome-wide maps of nuclear lamina interactions in single human cells. (DamID LaminB1, clone-5-5, diploid)

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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.

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Project description:In mammalian nuclei, transcriptionally active genomic regions tend to localize to the interior of the nucleus while inactive regions are often located at at the nuclear lamina. In this study we activated specific genes in lamina-associated domains by TALE-VP64 or CRISPRa-mediated activation. We also reduced transcription of individual genes by knockout of promoter/enhancer regions, or by insertion of a transcription termination sequence. In each case we generated genome-wide DamID maps to determine changes in nuclear lamina interactions, and in selected cases we also generated Repli-seq maps and/or RNAseq data.

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