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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Investigating genomic stability of the R26 EYFP locus in MEFs after Cas9-induced DSB

ABSTRACT: To exclude big genomic variations, we assessed the presence of low-frequency genomic changes using High-depth sequencing.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Mus musculus

SUBMITTER: Data Submission IFOM - ETS

PROVIDER: E-MTAB-16485 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Detecting EYFP RNA transcripts by Oxford Nanopore Technology in MEF R26 EYFP

Project description:We performed Nanopore direct sequencing in MEF R26 EYFP cells on a GridION device to detect EYFP RNA levels after DSB induction

2026-05-15 | E-MTAB-16775 | biostudies-arrayexpress

RNA-seq of mouse pancreatic pericytes from MyD88-deficient and control mice

Project description:To define pericytic MyD88-dependent expression of cytokines and other immune mediators, pancreatic pericytes were isolated based on their YFP-labeling from Nkx3.2-Cre;EYFP and Nkx3.2-Cre;EYFP;MyD88 flox/flox transgenic mice.

2023-12-31 | E-MTAB-13639 | biostudies-arrayexpress

Investigating genomic stability of the R26 EYFP locus in MEFs after Cas9-induced DSB

Project description:Investigating genomic stability of the R26 EYFP locus in MEFs after Cas9-induced DSB

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Fibroblastic reticular cells serve as primary immune checkpoint in visceral adipose tissues and secure peritoneal immunity

Project description:Immune protection of the body cavities depends on the swift activation of innate and adaptive immune responses in non-classical secondary lymphoid organs known as fat-associated lymphoid clusters (FALCs). While it is well-established that fibroblastic reticular cells (FRCs) are an integral component of the immune-stimulating infrastructure of lymph nodes and other classical secondary lymphoid organs, it has remained elusive whether and how FRCs in FALCs contribute to peritoneal immunity. Using FRC-specific gene targeting, we found that FALCs are underpinned by an elaborated FRC network and that initiation of peritoneal immunity was governed through FRC activation via MyD88-dependent innate immunological sensing. FRC-specific ablation of Myd88 expression blocked recruitment of inflammatory monocytes into FALCs and subsequent CD4+ T cell-dependent B-cell activation. Moreover, containment of Salmonella infection was compromised in conditionally Myd88-deficient mice indicating that FRCs in FALCs function as initial checkpoint in the orchestration of protective immune responses in the peritoneal cavity.

2018-06-12 | E-MTAB-6886 | biostudies-arrayexpress

Meis homeobox genes control cell competence within the eye-specified neuroepithelium (RNA-seq)

Project description:Vertebrate eye is derived from the neuroepithelium, surface ectoderm, and extracellular mesenchyme. Eye-specified neuroepithelium forms the optic cup in which spatial separation of three domains is established, namely, the region of multipotent retinal progenitor cells (RPCs), the ciliary margin zone (CMZ) possessing both neurogenic and non-neurogenic potential, and the optic disc (OD), the interface between the optic stalk and the neuroretina. Here, we show by genetic ablation in the developing optic cup that Meis1 and Meis2 homeobox genes function redundantly to maintain the retinal progenitor pool while they simultaneously suppress the expression of genes characteristic of CMZ and OD fates. Furthermore, we demonstrate that Meis transcription factors bind the regulatory regions of RPC-, CMZ-, and OD-specific genes, thus providing a mechanistic insight into the Meis-dependent gene regulatory network. Our work uncovers the essential role of Meis1 and Meis2 as regulators of cell fate competence and guardians of spatial territories in the vertebrate eye.

2021-02-17 | E-MTAB-9143 | biostudies-arrayexpress

Detecting EYFP RNA transcripts by Oxford Nanopore Technology in MEF R26 EYFP

Project description:Detecting EYFP RNA transcripts by Oxford Nanopore Technology in MEF R26 EYFP

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Mcl-1 is a key determinant of breast cancer cell survival [copy number]

Project description:Copy number profile of cultured Breast Cancer cell line measured by Affymetrix SNPs microarrays Whole genome copy number profile of 2 breast cancer cell lines were analyzed using Affymetrix SNP6.0 arrays

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Expression data comparing KRas(G12D/+);CreT, R26(H1047R/+);KRas(G12D/+);CreT, and MMTV-Neu mouse mammary tumors

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2015-09-16 | E-GEOD-73073 | biostudies-arrayexpress

Transcription profiling of mouse E12.5 ePet-EYFP rostral and caudal serotonin (5HT) neurons purified by flow cytometry

Project description:The 5HT system is organized into rostral and caudal populations with discrete anatomical locations and opposite axonal trajectories in the developing hindbrain. 5HT neuron cell bodies in the rostral subdivision migrate to the midbrain and pons and extend ascending projections throughout the forebrain. 5HT cell bodies in the caudal subdivision migrate to the ventral medulla and caudal half of the pons and provide descending projections to the brainstem and spinal cord. Experiment Overall Design: We used microarrays to determine genes expressed by both rostral and caudal 5HT neurons as well as genes that are differentially expressed between rostral and caudal 5HT neurons at E12.5 when axon pathfinding and cell migration are underway. E12.5 neural tubes were isolated from ePet-EYFP embryos and dissected into a rostral domain (mesecephalic flexure to pontine flexure) and a caudal domain (pontine flexure to spinal cord). After cell dissociation (details under growth protocol), cells were subjected to fluorescent activated cell sorting (FACS) to obtain 4 cell populations. R+ = rostral ePetEYFP positive 5HT neurons; R- = YFP negative non-serotonergic cells in the rostral neural tube; C+ = caudal ePetEYFP positive 5HT neurons; C- = YFP negative non-serotonergic cells in the caudal neural tube. 200,000 cells for each of the 4 cell types (R+, R-, C+, C-) were collected for RNA extraction and hybridization to Affymetrix Mouse 430 2.0 arrays.

2010-01-30 | E-GEOD-19474 | biostudies-arrayexpress

Genomic characterization of the MPNST

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2011-11-26 | E-GEOD-33881 | biostudies-arrayexpress

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