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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA sequencing in islets from Rip-Cre CDK8fl/fl and CDK8fl/fl mice with or without metabolic stress.

ABSTRACT: mRNA of pancreatic islets from Rip-Cre CDK8fl/fl and CDK8fl/fl mice were sequenced to investigate the consequence of genetic CDK8 ablation on genome wide transcript levels. Additionally, Rip-Cre CDK8fl/fl and CDK8fl/fl mice were stressed with STZ and then islets from those mice were sequenced to describe the transcriptome-wide regulation of beta-cells under stress condition.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Jing Xue

PROVIDER: E-MTAB-8201 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA sequencing in islets from Rip-Cre CDK8fl/fl and CDK8fl/fl mice with or without metabolic stress.

Project description:RNA sequencing in islets from Rip-Cre CDK8fl/fl and CDK8fl/fl mice with or without metabolic stress.

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2023-06-29 | E-MTAB-11393 | biostudies-arrayexpress

RNA-seq of islet, FACS- sorted CD45+Ly6C-CD11B+CD11C+F4/80+ cells from C57bl6/J male mice that were treated with low dose streptozotocin (STZ) or acetate buffer

Project description:The experiment was designed to obtain a broader unbiased view of the changes in islet macrophages following low dose STZ challenge. Mice were purchased from Jackson Laboratory (Bar Harbor, ME). 16-20-week-old C57BL/6J males were given 30 mg/kg STZ or acetate buffer (control) i.p. (intraperitoneal injection) for 5 consecutive days. Following the first STZ or buffer injection mice were sacrificed on day 14 and islets were isolated by collagenase digestion. Freshly isolated islets were dispersed in 0.02% Trypsin-EDTA for 3 minutes followed by up to 1 minute of pipetting under a stereomicroscope to obtain a single cell solution. Islet media was added to stop the reaction. Islets from 10 mice were pooled per sample (N). Dispersed islets were washed with FACS buffer (1% heat inactivated FBS, 1 mM EDTA, 11 mM glucose in PBS). Cells were kept on ice and pre-incubated with Fc Block (1:100) for 5 minutes, followed by 30 min incubation with CD45-eFluor 450 (1:250; clone 30-F11), Ly-6C-APC (1:1,200; clone HK1.4), CD11b-PE (1:1,200; clone M1/700, F4/80-FITC (1:150; clone BM8), CD11c-PECy7 (1:150; clone N418), and the viability dye 7AAD (1:2,000). Unstained, single stains, and fluorescence minus one controls were used for setting gates and compensation. Viable, single CD45+Ly6c-Cd11b+Cd11c+F4/80+ cells were sorted using a BD FACS Aria IIu directly into lysis buffer, and the RNeasy Plus Micro Kit from Qiagen was used to isolate total RNA. Total RNA quality control quantification was performed using an Agilent 2100 Bioanalyzer. All RNA samples had an RNA integrity number (RIN) ≥9.1. The NeoPrep Library Prep System from Ilumina was used for library preparation followed by sequencing using standard Illumina methods and Ilumina NextSeq500.

2019-11-01 | E-MTAB-7234 | biostudies-arrayexpress

RNA-seq of colonic tissues from Hif1a(fl/fl) and Ncr1(Cre)Hif1a(fl/fl) mice

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RNA-seq of small intestine tissues from Hif1a(fl/fl) and Ncr1(Cre)Hif1a(fl/fl) mice

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RNA-seq for blood Ly6Chi and Ly6Clo monocyte in WT and RBP-Jfl/fl Lyz2-Cre mice

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Atp4b-Cre;Cdh1(fl/fl);Kras(LSL-G12D/+);Trp53(fl/fl);Rosa26(LSL-YFP/LSL-YFP) mouse stomach vs. Atp4b-Cre;Cdh1(fl/+);Kras(LSL-G12D/+);Trp53(fl/fl);Rosa26(LSL-YFP/LSL-YFP) mouse stomach microarray

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2018-05-01 | E-MTAB-5833 | biostudies-arrayexpress

Single Cell RNA Sequencing of WT and Cdh5-cre Myct1 fl/fl Endothelium

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Expression data from pancreatic islets from Men1flf RIP-Cre mice, Rbp2flf RIP-Cre mice, Men1flf Rbp2flf RIP-Cre mice and matched control.

Project description:The menin tumor suppressor protein (Men1) is deficient in many endocrine tumors and forms an active complex with MLL family histone methyltransferases. This Men1 complex promotes histone H3 lysine 4 trimethylation at target loci including homeobox genes and cyclin-dependent kinase inhibitor genes. The loss of Men1 may be tumorigenic because it leads to decreased histone H3 lysine 4 trimethylation resulting in expressional changes of specific genes. Reversing tumorigenesis induced by a Men1 deficiency might be achieved by inhibition of histone H3 lysine 4 demethylase Rbp2 (Kdm5a). To this end, pancreatic islets from Men1f|f, Rbp2f|f and Men1f|f Rbp2f|f mice were expression profiled to determine what transcriptional changes induced by a Men1 deficiency are reversed by the loss of Rpb2. Pancreatic islets were isolated from Men1flf RIP-Cre mice, Rbp2flf RIP-Cre mice, Men1flf Rbp2flf RIP-Cre mice and two month old matched control mice. Total mRNA was extracted from islets and expression profiled on microarrays.

2011-07-25 | E-GEOD-26978 | biostudies-arrayexpress

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