Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Old_LSK_ATAC_seq

ABSTRACT: LSK (Lin-c-Kit+Sca1+) cells sorted from old Setd2 deficiency mice and control mice were used for ATAC sequencing.

TISSUE(S): ['bone Marrow']

SUBMITTER: Yuanliang Zhang

PROVIDER: OEX00027259 | NODE | 2024-02-27

REPOSITORIES: NODE

ACCESS DATA

Json Xml

Similar Datasets

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

H3K36 methyltransferase SETD2 regulates lymphoid and neural development [seq]

Project description:We study the role of loss of Setd2 and H3K36me3 in early B cell development through NGS methods including RNA, ChIP and ATAC Seq of sorted B cell populations of control and Setd2KO primary B cells from mice.

2020-03-23 | GSE130904 | GEO

Harnessing matrix stiffness to engineer a bone marrow niche for hematopoietic stem cell rejuvenation

Project description:RNA and ATAC sequencing data of primary sorting CD45-Ter119-CD31-Scf; GFP+Cxcl12; DsRed+ bone marrow stromal cells ,2D cultured bone marrow stromal cells and 3D cultured bone marrow stromal cells. RNA sequencing data of sorted primary and 3D cocultured Lin-Sca1+C-kit+CD150+CD48+ hematopoietic stem cells from 8-12 weeks and 12-13 months old mice. RNA and ATAC sequencing data of primary sorting CD45-Ter119-CD31-Pdgfra+td-Tomato+ bone marrow stromal cells from young (8 wks), middle aged (12 months) and aged (22-24 months) Lepr-Cre;td-Tomato mice.

2023-04-06 | GSE180866 | GEO

Single-cell RNAseq (10x Genomics) analysis of mouse splenic CD4+ T cells in WT and ∆Foxp3 mice and in WT/∆Foxp3 bone marrow chimeras

Project description:Single-cell RNAseq (10x Genomics) analysis of mouse splenic CD4+ T cells in WT and ∆Foxp3 mice and in WT/∆Foxp3 bone marrow chimeras. Mouse CD4+T cells in 21-day-old male WT and ∆Foxp3 mice were isolated from spleen by flow cytometry as DAPI–TCRβ+CD4+ cells for 10x Genomics Single Cell 3′ Reagent Kit (V2 chemistry, one sample per channel). For bone marrow chimera experiment: 7 week-old CD45.2-recipient mice were irradiated with 1000 Rad, reconstituted with 4 million CD3-depleted bone marrow cells: 50% CD45.1 x Foxp3-IRES-GFP (WT, 21d-old male) and 50% Foxp3DeltaEGFPiCre/RFP x ROSA-YFP x CD45.1/2 (scurfy, 21d-old male). 10 weeks later, spleen were harvested and tagged using a different Hashtags fo each mouse. ∆Foxp3 CD4+ T cells were sorted as DAPI–TCRb+CD4+CD45.1+CD45.2+. WT CD4+ T cells were sorted as DAPI–TCRb+CD4+CD45.1+CD45.2–. Control WT DAPI–TCRb+CD4+GFP+ Treg cells and GFP- Tconvs cells were also tagged and sorted. Samples with different hastags were pooled before single cell encapsulation using 10x Genomics Single Cell 3′ Reagent Kit (V3 chemistry).

2021-02-26 | GSE167575 | GEO

Niche stiffening compromises stem cell potential during aging by reducing chromatin accessibility at bivalent promoters

Project description:RNA and ATAC sequencing data of CD34+ Ia6+ sorted hair follicle stem cells from 6 and 24 months old mice

2021-05-06 | GSE148619 | GEO

Regulation of group 3 innate lymphoid cells by Setd2 [ATAC-seq]

Project description:To determine the molecular regulation of different subsets of ILC3s by Setd2, small intestinal NKp46- ILC3s (Thy1highCD45low NKp46-) and NKp46+ ILC3s (Thy1highCD45low NKp46+) from Setd2-deficient and control mice were subjected to assay for ATAC-seq.

2022-02-23 | GSE182832 | GEO

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

Intestinal mRNA profiles of 2-month old control (APCmin) and APCmin; Setd2IEC-/- mice generated by deep sequencing

Project description:Setd2 catalyzes trimethylation of lysine 36 on histone H3. H3K36me3 is deposited mainly in the gene body and has recently been demonstrated to play a role in regulating transcriptional elongation and alternative splicing. We conduct deep sequencing in 2-month old control (APCmin) and APCmin; Setd2IEC-/- mice intestinal cells to understand the splicing events regulated by Setd2.

2017-09-01 | GSE95663 | GEO

Bulk RNA-seq analysis of PDAC tumor Cells

Project description:Orthotopic PDAC tumor were established with KPC and KPSC cells, respectively. After about 10-14 days, PDAC cells with Setd2-KO and Setd2-WT were sorted from orthotopic PDAC tumor by DPAI-CD45.2-Pdpn-Epcam+, and used for RNA preparation.

2024-08-07 | GSE196752 | GEO

Control vs Elp3-deficient mouse myeloid progenitors 6-plex TMT LC-MSMS

Project description:6-plex TMT LC-MSMS quantification of proteins in myeloid progenitors (Lineage- Sca1- Kit+ cells) isolated from the bone marrow of 8-12 week old male and female control and Elp3-deficient (Elp3fl/fl vav-iCreT/+) mice. Biological triplicates of each genotype were analyzed, each consisting of 1.10e6 cells from pools of 12-14 control (Elp3fl/fl) or 26-38 (Elp3-deficient) male and female mice.

2021-01-26 | PXD010486 | Pride

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