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RNAseq for CDK7 brown adipose tissue specific knockout mice under room temperature and 6 hrs cold exposure.

ABSTRACT: Purpose: The goal of this study are to compare global gene expression profile in brown adipose tissue in Cdk7 bKO and WT control mice at both RT and after 6 hours cold exposure Methods: Interscapular BAT pads were taken from 12-week-old CDK7 bKO and control littermates either at room temperature or after 6 hours of cold exposure with food. Mice were sacrificed at zeitgeber time 9. Total RNA was extracted with TRI Reagent (Sigma). Two RNA samples from two mice with same genotype and condition were pool together (each 250 ng) to constitute 500 ng of total RNA from biological triplicates (three WT-RT, three CDK7 bKO-RT, three WT-cold, and three CDK7 bKO-cold) for sequencing. Results: Reads were also aligned to the Mus musculus.GRCm38.86 transcriptome using STAR (v. 2.5.2b, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011). Conclusions: Differentially expressed genes (DEGs) were identified between genotype and treatment.

ORGANISM(S): Mus musculus

PROVIDER: GSE149124 | GEO | 2020/05/20

REPOSITORIES: GEO

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RNAseq for perigonadal WAT of adipose tissue specific CDK7 knockout mice under CL or saline treatment for 7 days.

Project description:Purpose: The goal of this study are to compare global gene expression profile in pgWAT in Cdk7 aKO and WT control mice after CL or saline treatment for 7 days. Methods: pgWAT pads were taken from 9-week-old CDK7 aKO and control littermates either treated with CL or saline control for 7 days. Mice were sacrificed at zeitgeber time 9. Total RNA was extracted with TRI Reagent (Sigma). Two RNA samples from two mice with same genotype and condition were pool together (each 250 ng) to constitute 500 ng of total RNA from biological triplicates for sequencing. Results: Reads were also aligned to the Mus musculus.GRCm38.86 transcriptome using STAR (v. 2.5.2b, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011). Conclusions: Differentially expressed genes (DEGs) were identified between genotype and treatment.

2020-05-20 | GSE149123 | GEO

Transcriptional effects of KLF15 deletion in brown adipose tissue in response to fasting and cold

Project description:We report bulk RNA-sequencing of brown adipose tissue (BAT) harvested from K15flox/flox and BAT specific KLF15 knockout (K15-BKO) mice in response to cold challenge and fasting

2022-10-19 | GSE178720 | GEO

Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development

Project description:Gene expression profiles of sorted mammary epithelial cells from animals at 4, 6, and 8 weeks of age. Each individual sample was RNA obtained from an individual mouse. Our mice are mammary epithelium specific knocknout mouse models for gene Cobra1 and/or Brca1. For Cobra1, the first four exons were floxed. For Brca1, the largest exon, exon 11, was floxed. The mammary epithelium specific deletions were driven by cre recombinase under MMTV promoter (MMTV-cre). Animal genotype abbreviations used: wild-type (WT), meaning one of the following three: Cobra1f/f (Cff), Brca1f/f (Bff), and Brca1f/f;Cobra1f/f (Dff). Brca1 knockout (BKO), meaning MMTV-cre;Brca1f/f. Cobra1 knockout (CKO), meaning MMTV-cre;Cobra1f/f. Brca1 and Cobra1 double knockout (DKO), meaning MMTV-cre;Brca1f/f;Cobra1f/f

2016-03-18 | GSE67440 | GEO

Targeting transcriptional dependencies in cancer using a covalent CDK7 inhibitor (expression)

Project description:Cyclin-dependent kinase 7 (CDK7) plays a critical role in the general regulation of RNA polymerase II-mediated transcription. However, the absence of selective CDK7 inhibitors has hindered the ability to investigate the consequences of acute and prolonged inhibition of CDK7 under normal and pathological conditions. Here we present the discovery and characterization of the first covalent CDK7 inhibitor, CDK7-IN-1, that has the unprecedented ability to target a unique cysteine residue located outside of the canonical kinase domain, providing an unanticipated means of achieving selectivity for CDK7 amongst the 20 known CDKs. Cancer cell line profiling indicates that a subset of cancer cell lines, including T-cell acute lymphoblastic leukemia (T-ALL), exhibit 100-fold greater sensitivity to CDK7-IN-1 over other tumor and normal cell lines. Genome-wide expression analysis in Jurkat T-ALL indicates that CDK7-IN-1 disproportionally affects RUNX1 as well as other components of the TAL1 transcriptional network and its targets, downregulating key regulators of transcription and apoptosis critical for the T-ALL state. These oncogenes are encoded by short-lived mRNA transcripts, are associated with super-enhancers, and exhibit a strong dependency on continuous transcription for sustained expression. Therefore, pharmacological modulation of CDK7 kinase activity may define a method for the identification and treatment of tumor types exhibiting extreme dependencies on transcription for maintenance of the oncogenic state. Jurkat, MM1S, Loucy, and HeLa (WT and Dox-inducible CDK7 mutant) cells were treated with various drugs including a covalent inhibitor of CDK7 (CDK7-IN-1), a reversible inhibitor of CDK7 (CDK7-IN-1), Flavopiridol, Actinomycin D, and DMSO controls. Replicates are annotated.

2014-06-22 | E-GEOD-50624 | biostudies-arrayexpress

Next Generation Sequencing Facilitating Quantitative Analysis of Wild Type (Kcnj11fl/fl, WT) and β-cell Specific Kcnj11 -/- (βKcnj11 -/-, bKO) Mouse Islets' Transcriptomes

Project description:β-cell Specific Kcnj11 -/- mice and their islets exhibited a hirtherto unkown switch in the major signaling pathway of G-protein coulpled receptors from Gs to Gq, and overall enhanced Gq signaling. That the phenomeno was also observed in their isolated islets, and that the genetic manipulation of the mice was only in the pancreatic beta-cells, we reasoned that peharps knockout of Kcnj11 in beta cells could result to a general change in the expression of genes related to G-protein coupled receptor signaling. Since New-Generation Sequencing (NGS) has revolutionized cellular based pathway analysis, we extracted total RNA from WT and bKO islets, performed NGS and compared global changes in the expression of genes between WT and bKO islets.

2021-04-24 | GSE156917 | GEO

Nalm 6 WT; Nalm6 BKO; Nalm 6 A hets

Project description:Nalm 6 WT; Nalm6 BKO; Nalm 6 A hets

| PRJNA623327 | ENA

Expression data from CSF1- or CSF2-induced bone marrow derived macrophages (BMDMs): M(CSF1) and M(CSF2) cells.

Project description:Femur and tibia bones were harvested from 8-week-old wild-type (WT) C57BL/6 mice. Bone marrow was flushed out into cold PBS (Life Technologies) plus 2% heat-inactivated FBS, passed through a needle five times to dissociate the cells, and then passed through a 70-μm cell strainer (Becton Dickinson) to remove cell clumps, bone, hair, and other cells/tissues. After addition of three volumes of NH4Cl solution (0.8% NH4Cl solution; Beyotime Institute of Biotechnology, Jiangsu, China), the mixture was incubated on ice for 10 min to remove red blood cells; the cells were then spun down and resuspended in cold PBS with 2% FBS. The harvested cells were cultured in DMEM containing 10% FBS and supplemented with 10 ng/ml recombinant mouse CSF1 (R&D Systems) or 10 ng/ml recombinant mouse CSF2 (R&D Systems) for 7 days to obtain CSF1- or CSF2-induced BMDMs: M(CSF1) or M(CSF2) cells, respectively. To test the difference genes expression of TAMs obtained from M(CSF1) and M(CSF2) cells in C57BL/6 mice. We used microarrays to detail the global programme of gene expression and identified M(CSF1) and M(CSF2) cells during this process.

2017-02-28 | GSE95404 | GEO

Single-nucleus transcriptome analysis of interscapular brown adipose tissue (iBAT) in Wtapflox/flox and BAT-specific Wtap knockout (BKO) mice

Project description:Purpose: Through Single-nucleus transcriptome analysis, we aim to characterize the changes of cell heterogeneity in iBAT obtained from Wtap-BKO mice compared with that in Wtapflox/flox mice. Methods: Nuclei were isolated from iBAT of Wtap flox/flox and Wtap-BKO mice at 8 weeks old. Each sample was pooled from 4 mice for each group. Conclusion: The Single-nucleus transcriptomes of iBAT in Wtapflox/flox and BKO mice were characterized.

2022-10-20 | GSE202630 | GEO

microRNA profiling of murine wt and MyD88-/- deficient bone marrow derived macrophages upon infection with Legionella Pneumophila

Project description:wt and MyD88-/- murine bone marrow derived macrophages were infected with Legionella Pneumophila for 24h. RNA was isolated by phenol/chloroform precipitation. 400 ng RNA per sample were then reverse transcribed with the Life Technologies miR RT kit with megaplex primers. Reverse transcribed RNA was then loaded on the rodent Taqman Low Density Array (TLDA) Cards and run according to manufacturer´s recommendations

2017-06-12 | GSE92600 | GEO

Transcriptome and metabolome changes in Chinese cedar during cold acclimation reveal the roles of flavonoids in needle discoloration and cold resistance

Project description:Cryptomeria fortunei growth and development are usually affected by low temperatures. Despite the evergreen nature of this species, most needles turn yellowish-brown in cold winters. The underlying discoloration mechanisms that cause this phenomenon in response to cold acclimation remain poorly understood. Here, we measured the pigment content and ultrastructure of normal wild-type (Wt) and evergreen mutant (GM) C. fortunei needles and performed integrated transcriptomic and metabolomic analyses to explore potential discoloration mechanisms. The results showed that the needle chlorophyll content of these two genotypes decreased in winter. Wt needles showed greater decrease in the chlorophyll content and local destruction of chloroplast ultrastructure, and contained larger amounts of flavonoids than GM needles, as shown by metabolomics analysis. We subsequently identified key differentially expressed genes in the flavonoid biosynthesis pathway and observed significantly upregulated flavonol synthase (FLS) expression in Wt needles compared to GM needles, that significantly increased the anthoxanthin (flavones and flavonols) content, which is likely a key factor underlying the difference in needle color between these two genotypes. Therefore, flavonoid metabolism may play important roles in the cold resistance and needle discoloration of C. fortunei, and our results provide an excellent foundation for the molecular mechanism of C. fortunei in response to cold stress.

2022-08-12 | MTBLS3184 | MetaboLights

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