Baf250a orchestrates an epigenetic pathway to repress the Nkx2.5-directed contractile cardiomyocyte program in the sinoatrial node
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Yong Zhao
PROVIDER: E-GEOD-55682 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:We specifically deleted Baf250a in the SAN by using Hcn4-CreERT2 mice. We performed mRNA-seq to identify dysregulated genes in the SAN after deletion of Baf250a. To identify direct targets of Baf250a and sequential transcriptional events after deletion of Baf250a in the SAN, we performed mRNA-seq at 6 time points. i.e. 0 hr (tamoxifen treatment), 16 hr after tamoxifen treatment, 20 hr, 24 hr, 48 hr, and 6 days after tamoxifen treatment.
2016-03-22 | GSE55682 | GEO
Project description:Long-term tamoxifen treatment significantly improves the survival of hormone receptor-positive (HR+) breast cancer (BC) patients. However, tamoxifen resistance remains a big challenge for endocrine therapy. We aimed to identify prognostic biomarkers for tamoxifen treatment and explore their role in tamoxifen resistance. We used Exiqon miRCURY™ LNA Array (v.18.0) to detect the miRNA expression profiles in the primary tumors and their matched recurrent/metastatic lesions from six HR+ breast cancer patients who relapsed after TAM treatment. Fold changes ≥ 2 and P values < 0.05 were defined as differential expression. We found that 28 miRNAs were significantly downregulated in recurrent/metastatic lesions compared to primary tumors, and 54 miRNAs were significantly upregulated.
2016-12-29 | GSE83292 | GEO
Project description:Purpose: The goals of this study are to identify dysregulated mRNAs in the heart after deletion of miR-1-1 and miR-1-2. Methods: Total RNAs were extracted from hearts at embryonic E15.5 (E15.5) or postnatal 2.5 days (P2.5) of miR-1s dHET and miR-1s dKO mice. mRNAs were purified using a poly-A selection approach and sequenced using Illumina HiSeq 2000. The sequence reads were aligned to the mouse reference genome (NCBI Build 37/mm9) using TopHat program (Bowtie algorithm). Transcript assembles and identification of differentially expressed genes were achieved using Cufflinks package. To account for expression bias due to transcript length, each sample transcript expression was normalized by using cufflinks algorithm with a FDR of 0.05. Results: Using 1.5-fold change as a cutoff, 997 and 653 transcripts were found to be upregulated and downregulated, respectively, in miR-1s dKO heart at P2.5. 423 transcripts were found to be upregulated and 653 were down-regulated in miR-1s dKO heart at E15.5. Many upregulated genes are directly involved in a fetal gene program. Conclusions: miR-1 directly represses a fetal gene program. We performed RNA deep-seq using postnatal 2.5 days (P2.5) heart from miR-1-1 and miR-1-2 double knockout mice and compared it to that of littermate control.
2014-03-26 | E-GEOD-45760 | biostudies-arrayexpress
Project description:We employed high-throughput sequencing of both short (~18-24nt) and long (>200nt) RNAs in human erythrocytes. We obtained blood from five healthy individuals for the short (small) RNA-seq library preparations and blood from three individuals for the long RNA-seq library preparations. We identified an abundant, diverse population of RNAs. Both polyadenylated and nonpolyadenlated long RNAs were identified. Additionally, known and novel microRNAs were identified in the short RNA dataset using the probabalistic modeling algorithm miRDeep. These RNAs lend insight into erythrocyte biology and provide utility as potential biomarkers. To determine both shared and unique aspects of the erythrocyte long RNA transcriptome, we compared this transcriptome with that of the PBMC and CD34+ erythroid progenitor transcriptomes. Sequencing of RNAs from mature erythrocytes of healthy individuals
2015-11-19 | E-GEOD-63703 | biostudies-arrayexpress
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2016-08-01 | E-GEOD-78199 | biostudies-arrayexpress
Project description:Background: Geographic variation in the thermal environment impacts a broad range of biochemical and physiological processes and can be a major selective force leading to local population adaptation. In the intertidal copepod Tigriopus californicus, populations along the coast of California show differences in thermal tolerance that are consistent with adaptation, i.e., southern populations withstand thermal stresses that are lethal to northern populations. To understand the genetic basis of these physiological differences, we use an RNA-seq approach to compare genome-wide patterns of gene expression in two populations known to differ in thermal tolerance. Results: Observed differences in gene expression between the southern (San Diego) and the northern (Santa Cruz) populations included both the number of affected loci as well as the identity of these loci. However, the most pronounced differences concerned the amplitude of up-regulation of genes producing heat shock proteins (Hsps) and genes involved in ubiquitination and proteolysis. Cuticle genes were up-regulated in SD but down-regulated in SC, and mitochondrial genes were downregulated in both populations. Among the hsp genes, orthologous pairs show markedly different thermal responses as the amplitude of hsp response was greatly elevated in the San Diego population, most notably in members of the hsp70 gene family. There was no evidence of accelerated evolution at the sequence level for hsp genes. Conclusions: Marked changes in gene expression were observed in response to acute sublethal thermal stress in the copepod T. californicus. Although some qualitative differences were observed between populations (e.g., cuticle gene regulation), the most pronounced differences involved the magnitude of induction of numerous hsp and ubiquitin genes. These differences in gene expression suggest that evolutionary divergence in the regulatory pathway(s) involved in acute temperature stress may offer at least a partial explanation of latitudinal trends in thermal tolerance observed in Tigriopus. For each population, ~600 copepods were split into two equal samples, one for control and one for treatment. Each sample was placed in a 50 mL Falcon tube containing 30 mL filtered seawater. After equilibrating samples to 20 degrees C, each tube was immersed in water bath at its target temperature (control: 20 C; treatment: 35 C) for one hour, and then immersed at 20 C for one hour for recovery. Copepods were then collected in a net mesh and quickly transferred to a tube containing 5 mL Tri-reagent for standard RNA extraction.
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Project description:Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples. Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods. 8 mouse embryonic stem cell samples, 4 control and 4 cisplatin treated, 4 replicates per group for Affymetrix arrays. Of these, 6 were used for sequencing and are reported in this Series.
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