Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub, H3K27me3 and H3K36me3 in KPC1199 murine PDAC cell line

ABSTRACT: To gain mechanistic insight into how Epigenetic factors reprogramming metabolism in response to glutamine starvation. we performed CUT&Tag sequencing in murine PDAC cells. KPC1199 cells were treated in Cont group or Low Gln group , and harvested after 72 hours. CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme). DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme).

ORGANISM(S): Mus musculus

PROVIDER: GSE229903 | GEO | 2024/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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.

2023-02-06 | GSE176013 | GEO

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.

2024-08-20 | GSE222133 | GEO

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.

2024-08-07 | GSE196241 | GEO

ATAC-seq analysis in KPC1199 murine PDAC cell line with or without glutamine starvation

Project description:We determined if up- and/or down-regulated genes in pancreatic tumor cells cultured under low-glutamine conditions were accompanied by alterations in genome-wide chromatin accessibility and then performed ATAC-seq of KPC1199 cells treated with low glutamine concentrations versus normal-media-treated controls. The ATAC-seq was performed according to the TruePrep Tagment Enzyme for ATACseq kit (TD501, Vazyme). DNA libraries were constructed following the manufacturer’s instructions of the Trueprep index kit v2 (TD202, Vazyme) and thereafter sequenced to an average of 20 million reads per sample.

2024-04-30 | GSE229051 | GEO

The role of compensatory metabolic reprogramming in ensuring PDAC cell survival under the limitation of glutamine

Project description:KPC1199 cells were treated in Cont group(2 mmol/L glutamine and 2.25 g/L glucose) or Low Gln group (0.4 mmol/L glutamine and 2.25 g/L glucose) , and harvested after 72 hours for RNA preparation.

2024-12-31 | GSE229055 | GEO

Genome-wide mapping of MEF2A binding sites by CUT&Tag-seq in chicken primary myoblasts

Project description:In this study, CUT&Tag-seq technology was employed to investigate MEF2A binding sites across the entire genome of chicken primary myoblasts. CUT&Tag was performed using CUT&Tag Assay Kit for Illumina Pro (TD904-1) from Vazyme. Antibody targeting MEF2A as well as IgG were used.The final DNA library on a HiSeq PE150 platform was subjected for the analyses. This study provides a wide landscape of MEF2A target genes from chicken primary myoblasts, which supports the active role of MEF2A in avian muscle development.

2023-12-05 | GSE249097 | GEO

CUT&Tag of mouse primary B cells transduced Pbx1 overexpression plasmid.

Project description:We performed the cleavage under targets and tagmentation (Cut & tag) assay followed by sequencing enriched DNA fragments to reveal the direct downstream targets of Pbx1. Firstly, we overexpressed Pbx1b with Pbx1b-IRES-GFP retrovirus in murine peripheral B cells to ensure the yields of DNA fragments. CUT & tag libraries were generated following instructions of the manufacturer’s protocol (Vazyme; cat TD901-01) and the Pbx1 antibody (CST; cat 4342) was used for signal enrichment.

2023-03-26 | E-MTAB-12769 | biostudies-arrayexpress

Single cell RNA Sequencing Analysis of Gene Expression Profile in Dgcr8 Conditional KO Embryonic Hearts

Project description:Purpose: To compare the single cell transcriptome of wild type and Mesp1Cre+/Dgcr8-/- embryonic heart at embryonic stage E9.5 Methods: For single cell sample preparation, Ventricular part of E9.5 heart tubes were dissected and digested into single cells by 0.04% Trypsin combined with 0.05% Collagenase IV, and then transferred into DMEM containing 10% fetal bovine serum for termination. After washed in PBS without Ca2+, the single cells were manually transferred into cell lysis buffer with a mouth pipette. Total RNA was reverse transcribed and amplified using Smart-seq2 protocol (Picelli et al., 2014), followed by Tn5 tagmentation and PCR enrichment to generate libraries using TruePrep DNA Library Prep Kit V2 for illumina (Vazyme, TD501-503) according to the manufacturer’s suggested protocol. Clean reads were mapped to mouse genome (mm10) using Salmon. Results: Genes significantly differentially expressed in the E9.5 Dgcr8 cKO single cardiomyocyte compared with wild type group were identified. Conclusions: Dgcr8 cKO caused important gene expression changes in E9.5 cardiomyocytes at single cell level

2018-09-12 | GSE110265 | GEO

Dissection of anterior mesendoderm segregation at single cell level in zebrafish

Project description:Purpose: To investigate Ripply1 binding site in zebrafish embryo Methods: HA-ripply-injected embryos were harvested at 6hpf. CUT&Tag were performed on the collected cells using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904) following the protocol.The products were sent for paired-end sequencing at 150 bp read length on a NovaSeq 6000 system. Results: 72,683 peaks were enriched in HA-ripply1-injected samples. And Ripply1 binding peaks were found to be enriched in the immediate upstream region of the gene body of sox17 and sox32. Conclusions: Ripply1 may repress sox17 and sox32 expression through direct binding.

2023-12-06 | GSE249292 | GEO

Af-CUT&Tag: A Sensitive and Antibody-Free Chromatin Profiling Method Using Genetically Encoded Tags and High-Affinity Binders III

Project description:Transcription factors and chromatin features play critical roles in regulating gene expression. Experimental methods used for highly sensitive chromatin-binding protein profiling, such as CUT&Tag, are limited due to their high cost and technical restrictions, thereby impeding their widespread application. Therefore, we pioneered an antibody-free and sensitive tool for epigenetic analysis, Af-CUT&Tag. Application of the method requires prior generation of cell expressing a protein of interest (POI) tagged C-terminal short peptides. By leveraging the picomolar affinity between peptide and its binder, Tn5 fused with binder can specifically and highly sensitively recognize the peptide tagging protein. We show that the Af-CUT&Tag method is straightforward and can be applied to different proteins across cell lines and tissues, and extendable to single-cell analysis. With only minimal amounts of cellular or tissue material, it provides high sensitivity and yields abundant chromatin fragments per cell and offers unique insights into the regulation of early liver regeneration by the Hippo signaling pathway at the single-cell level. Together, we demonstrate that Af-CUT&Tag is a universal and comprehensive epigenetic analysis tool that can be extended to peptide and peptide-binding nanobody-Tn5 for epigenetic analysis.

2024-12-15 | GSE283706 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data