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CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub and H3K27me3 in treated KPC1199 murine PDAC cell line

ABSTRACT: CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub and H3K27me3 in treated KPC1199 murine PDAC cell line

PROVIDER: PRJNA918356 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22967754_1.fastq.gz	Fastqsanger.gz
	SRR22967754_2.fastq.gz	Fastqsanger.gz
	SRR22967755_1.fastq.gz	Fastqsanger.gz
	SRR22967755_2.fastq.gz	Fastqsanger.gz
	SRR22967756_1.fastq.gz	Fastqsanger.gz

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CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub and H3K27me3 in treated KPC1199 murine PDAC cell line

Project description:To gain mechanistic insight into how Epigenetic factors reprogramming tumor immune microenvironment in response to IFNγ stimulation. we performed CUT&Tag sequencing in murine PDAC cells.For comparison of the transcription profile between IFNγ-PD-L1all and IFNγ+PD-L1all cells, we treated KPC1199 cells with vehicle control or 10 ng/mL recombinant mouse IFNγ for 20 hours and harvested them. For comparison of PD-L1hi with PD-L1all, cells were either sorted with the top 15% PD-L1+ or total of IFNγ+PD-L1all PDAC cells, and freshly collected as soon as possible. Hyperactive pA-Tn5 Transposase for CUT&Tag kit from Vazyme (TD901), and antibodies against H3K4me3 from Abcam (ab213224), H3K27Ac from Abcam (ab4729),H2A119Ub from Cell Signaling (8240T) and H3K27me3 from Abcam (ab6002) were employed. Trueprep index kit v2 and v3 for illumina were used to establish DNA library.

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CUT&Tag sequencing in PDAC cells with Setd2-KO and Setd2-WT sorted from orthotopic PDAC tumor

Project description:To gain mechanistic insight into how Setd2 loss reprogramming tumor cell metabolism, we performed CUT&Tag sequencing in PDAC cells with Setd2-KO and Setd2-WT sorted from orthotopic PDAC tumor. Setd2-WT and -KO murine PDAC cells were sorted with DAPI-CD45.2-Pdpn-Epcam+ or cultured, and freshly collected as soon as possible. Hyperactive pA-Tn5 Transposase for CUT&Tag kit from Vazyme (TD901), and antibodies against H3K36me3, H3K27Ac and H3K27me3 were employed. Trueprep index kit v2 and v3 for illumina were used to establish DNA library.

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H3K27ac, H3K4me3, H3K27me3 and H3K9me3 ChIPseq of SKOV3(AA) and SKOV3(CC)

Project description:To study the effect of rs1192691 on histone modifications, we performed H3K27ac, H3K4me3, H3K27me3 and H3K9me3 in SKOV3(AA) and SKOV3(CC).

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CUT&Tag analysis of H3K36me3 and H3K27me3, in Setd2-WT and -KO murine PDAC cell line

Project description:To gain mechanistic insight into how Setd2 loss promotes activation of AKT signaling, we performed CUT&Tag sequencing in PDAC cells (KPC1199) with Setd2-KO and Setd2-WT). Setd2-WT and -KO murine PDAC cells were cultured and freshly collected as soon as possible. Hyperactive pA-Tn5 Transposase for CUT&Tag kit from Vazyme (TD901), and antibodies against H3K36me3 and H3K27me3 were employed. Trueprep index kit v2 and v3 for illumina were used to establish DNA library.

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Project description:Neurons are central to lifelong learning and memory, but ageing disrupts their morphology and function, leading to cognitive decline. Although epigenetic mechanisms are known to play crucial roles in learning and memory, neuron-specific genome-wide epigenetic maps into old age remain scarce, often being limited to whole-brain homogenates and confounded by glial cells. Here, we mapped H3K4me3, H3K27ac, and H3K27me3 in mouse neurons across their lifespan. This revealed stable H3K4me3 and global losses of H3K27ac and H3K27me3 into old age. We observed patterns of synaptic function gene deactivation, regulated through the loss of the active mark H3K27ac, but not H3K4me3. Alongside this, embryonic development loci lost repressive H3K27me3 in old age. This suggests a loss of a highly refined neuronal cellular identity linked to global chromatin reconfigu-ration. Collectively, these findings indicate a key role for epigenetic regulation in neurons that is inextricably linked with ageing.

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CUT&RUN-seq of H3K4me3, H3K27me3 and H3K27ac in mll2wt and mll2[Y2602A] mESC

Project description:CUT&RUN-seq of H3K4me3, H3K27me3 and H3K27ac in mouse ESCs carrying a homozygous point mutation in the catalytic domain of mll2[Y2602A]. CUT&RUN was performed according to Skene & Henikoff, 2017 and purified DNA was using for library preparation with NEBNext DNA Ultra II kit (NEB E7645S; input: 5 ng of DNA). Libraries were multiplexed and sequenced on a NextSeq500 (Paired-End; read length 40). Each sample is present in 3 biological replicates.

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CUT&Tag on H3K4me3, H3K27ac, H3K4me1, H3K9me3, H3K27me3, H3K36me3 and H2AK119ub in TX1072 XXΔXic and XO mESCs during differentiation

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| PRJNA704375 | ENA

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