Project description:Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells. Timepoints taken at Day 0 (AT2 cell), Days 2, 4, and 6 in culture (differentiating) and Day 8 in culture (AT1-like cells). 1ug of RNA was subjected to cRNA conversion using Illumina TotalPrep RNA kit and hybridized to the HT12v4 array Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells
Project description:Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells. Timepoints taken at Day 0 (AT2 cell), Days 2, 4, and 6 in culture (differentiating) and Day 8 in culture (AT1-like cells). 1ug of RNA was subjected to cRNA conversion using Illumina TotalPrep RNA kit and hybridized to the HT12v4 array Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells
Project description:Analysis of chromatin state during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells. Timepoints taken at Day 0 (AT2 cell), and Day 8 in culture (AT1-like cells). Examination of 2 different histone modifications in 2 cell types.
Project description:We profiled gene expression changes in differentiating i-Mixl1 ES cells(Willey, Ayuso-Sacido et al., 2006, Blood 107(8): 3122-3130) cultured in the presence or absence of Doxycycline (DOX, 0.1 ug/ml, 3 replicates per treatment/time point). Total RNA was isolated from EBs harvested at day 2, 3 and 4 (DOX added 1 day after plating of ES cells). RNA (1 ug) was subjected to one round of linear amplification (RiboAmp System) to yield 10 ug of RNA. The RNA was indirectly labeled using amino allyl-dUTP('t Hoen, de Kort et al., 2003, Nucleic Acids Res. 31: e20), then conjugated with Cy3 or Cy5. The labeled RNAs were used to screen a 15K mouse developmental cDNA microarray(Tanaka, Jaradat et al., 2000, Proc. Natl. Acad. Sci. U.S.A. 97: 9127-9132). Pairwise analysis of hybridization results for EBs cultured with or without DOX was performed for samples harvested on each day. Spotfire(R) software was used for data management and filtering. Gene expression ratios were normalized after filtering the data to remove low-intensity and poor quality spots. Data obtained for replicate samples were in excellent agreement. Six experiments total: three time points (day 2, day 3, day 4); for each time point mRNA was collected in the presence or absence of Doxycycline. Three biological replicas were collected for each of the six experiments
Project description:Polycomb complexes are essential regulators of stem cell identity, yet very little is known about their molecular mechanisms during cell differentiation. Pcgf proteins (Pcgf1/2/3/4/5/6) are core subunits of the Polycomb repressive complex 1 (PRC1). It has been recently proposed that specific Pcgf proteins are associated to particular PRC1 complexes, yet the molecular and biological functions of different Pcgf proteins remains largely elusive. Using specific differentiation protocols, we have elucidated a role for Pcgf2/Mel18 in specifically regulating mesoderm differentiation. Mechanistically, during early cardiac mesoderm differentiation, Pcgf2/Mel18 functions as a classical Polycomb protein by repressing pluripotency, lineage specification, late cardiac differentiation and negative regulators of the BMP pathway, yet Pcgf2/Mel18 also positively regulates the expression of key mesoderm transcription factors, revealing a novel function of Pcgf2/Mel18 in gene activation during cardiac differentiation. Mel18 depletion results in an unbalance of pathways that positively and negatively regulate cardiac differentiation. We propose that Mel18 is a novel epigenetic factor that controls mesoderm differentiation by opposing molecular mechanisms. List of ChIPseq samples: Mel18 in ESCs and MES, Ring1b, RYBP and Cbx2 in MES, IgG in MESs. List of RNAseq experiments: Mel18 KD, Ring1b KO and CTR in ESCs, Mel18 KD and CTR in MES, Mel18 KD and CTR in CMs.
Project description:Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts, while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1,133 non-coding multi-exonic transcripts expressed during embryogenesis. These include long intergenic ncRNAs (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for small RNAs (sRNAs). Zebrafish lncRNAs share many of the characteristics of their mammalian counterparts: relatively short length, low exon number, low expression, and conservation levels comparable to introns. Subsets of lncRNAs carry chromatin signatures characteristic of genes with developmental functions. The temporal expression profile of lncRNAs revealed two novel properties: lncRNAs are expressed in narrower time windows than protein-coding genes and are specifically enriched in early-stage embryos. In addition, several lncRNAs show tissue-specific expression and distinct subcellular localization patterns. Integrative computational analyses associated individual lncRNAs with specific pathways and functions, ranging from cell cycle regulation to morphogenesis. Our study provides the first comprehensive identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic and evolutionary studies. ChIP-Seq for H3K4me3 and H3K27me3 at zebrafish shield stage.
Project description:White fat browning is a highly variable genetic trait in mice (Guerra et al., 1998). To gain an overview of strain variations in browning capacities, we performed transcriptome analysis of white fat browning in (1) 5 inbred mouse strains (C57BL/6J, 129S6sv/ev, A/J, AKR/J, and SWR/J) with distinct browning propensities in WAT, and (2) F1 hybrids derived from a high (129S6sv/ev) and low browning strain (C57BL/6J) cross. White fat browning is a highly variable genetic trait in mice (Guerra et al., 1998). To gain an overview of strain variations in browning capacities, we performed transcriptome analysis of white fat browning in three genetic models (Figure 1A), including (1) 5 inbred mouse strains (C57BL/6J, 129S6sv/ev, A/J, AKR/J, and SWR/J) with distinct browning propensities in WAT, (2) F1 hybrids derived from a high (129S6sv/ev) and low browning strain (C57BL/6J) cross.
Project description:This SuperSeries is composed of the following subset Series: GSE32898: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq] GSE32899: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [ChIP_Seq] Refer to individual Series
Project description:Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. However, the contribution of AS to the control of embryonic stem cell (ESC) pluripotency is not well understood. Here, we identify an evolutionarily conserved ESC-specific AS event that changes the DNA binding preference of the forkhead family transcription factor FOXP1. We show that the ESC-specific isoform of FOXP1 stimulates the expression of transcription factor genes required for pluripotency including OCT4, NANOG, NR5A2 and GDF3, while concomitantly repressing genes required for ESC differentiation. Remarkably, this isoform also promotes the maintenance of ESC pluripotency and the efficient reprogramming of somatic cells to induced pluripotent stem cells. These results reveal an AS switch that plays a pivotal role in the regulation of pluripotency through the control of critical ESC-specific transcriptional programs. In order to identify AS events that potentially control stem cell pluripotency, we used microarray profiling to compare patterns of AS in undifferentiated and differentiated H9 human embryonic stem cells (hESCs).