Project description:Deep RNA sequceing was performed to explore the expression level of miRNAs in HeLa cell exosomes after treatment with or without 10 ng/ml TGF-β1 for 24 h. The results showed that 48 miRNAs were enriched in exosomes of HeLa cells after treated with TGF-β1 compared with non-treated cells (negative control), proving that TGF-β1 affects HeLa cell exosomes miRNA profile.
Project description:We monitored 9 pluripotent stem cell lines across three time points of hepatic directed differentiation, representing 3 developmental stages: undifferentiated (T0), definitive endoderm (T5), and early hepatocyte (T24). ESCs (n=3) and patient-derived normal (n=3) or PiZZ (n=3) iPSCs were analyzed in the undifferentiated state (T0), after differentiation to definitive endoderm (T5), and upon reaching hepatic stage (T24) for a total of 27 samples. We sought to test the hypothesis that a single transgene-free iPSC clone from each donor could be used to detect disease-specific differences between the normal cohort and the PiZZ cohort, anticipating that this difference would emerge only at a developmental stage in which the mutant AAT gene is expressed. Cells were sorted before analysis at T0 and T5 after antibody staining for TRA1-80+/SSEA3+ (T0) or C-kit+/CXCR4+ (T5) cells.
Project description:CD14+ Macrophage were challenged with Wildtype (WT), or S1154-deletion mutant (Del), and sequenced at timepoints zero hours (T0) and twenty-four hours (T24). To generate DEGs T0 and T24 timepoints were compared, a multifactor DESEQ2 run comparing T0 and T24 in both Wildtype and Deletion strains, and a direct comparison of T24 timepoints in Mutant and Deletion were generated.
Project description:Large-scale genomic studies have identified multiple somatic aberrations in breast cancer, including copy number alterations, and point mutations. Still, identifying causal variants and emergent vulnerabilities that arise as a consequence of genetic alterations remain major challenges. We performed whole genome shRNA "dropout screens" on 77 breast cancer cell lines. Using a hierarchical linear regression algorithm to score our screen results and integrate them with accompanying detailed genetic and proteomic information, we identify vulnerabilities in breast cancer, including candidate "drivers," and reveal general functional genomic properties of cancer cells. Comparisons of gene essentiality with drug sensitivity data suggest potential resistance mechanisms, effects of existing anti-cancer drugs, and opportunities for combination therapy. Finally, we demonstrate the utility of this large dataset by identifying BRD4 as a potential target in luminal breast cancer, and PIK3CA mutations as a resistance determinant for BET-inhibitors. The T0 measurements for the EFM19, HCC1954, HCC38 screens were omitted for technical reasons. T0 measurements, regardless of cell line, represent the initial abundance of shRNAs before cell line-specific selection effects, leading to highly correlated T0 measurements across cell lines. Our analyses showed a median correlation of 0.92 between pairs of T0 arrays from different cell lines, compared to correlations of 0.94-0.97 for replicate arrays within a cell line, a median correlation of 0.79 between T1 arrays of different cell lines and median correlation of 0.68 between T2 arrays from different cell lines. As a result, we used to T0 measurements of the MCF7 screen to provide initial shRNA abundance measurements for the HCC1954 and HCC38 screens, and T0 measurements from the SW527 screen to provide initial measurements for the EFM19 screen. Additional formatted data can be found at http://neellab.github.io/bfg/. Code and tutorials for the siMEM algorithm can be found at http://neellab.github.io/simem/.
Project description:We studied early events of flower formation with a temporal resolution by employing a floral induction system to drive synchronized flower development from inflorescence meristem-like tissue (Wellmer et al. (2006)). We generated a developmental time series including vegetative leaf tissue, young developing flowers at zero (t0) and two days after induction of flower development (t2), and fully expanded inflorescences. Although we found very similar numbers of H3K27me3 and H3K4me3 target genes, many genes display quantitative changes in those marks, especially between different tissue types (e.g. >60% of target genes change quantitatively from leaf to t0).
Project description:We monitored 9 pluripotent stem cell lines across three time points of hepatic directed differentiation, representing 3 developmental stages: undifferentiated (T0), definitive endoderm (T5), and early hepatocyte (T24). ESCs (n=3) and patient-derived normal (n=3) or PiZZ (n=3) iPSCs were analyzed in the undifferentiated state (T0), after differentiation to definitive endoderm (T5), and upon reaching hepatic stage (T24) for a total of 27 samples. We sought to test the hypothesis that a single transgene-free iPSC clone from each donor could be used to detect disease-specific differences between the normal cohort and the PiZZ cohort, anticipating that this difference would emerge only at a developmental stage in which the mutant AAT gene is expressed. Cells were sorted before analysis at T0 and T5 after antibody staining for TRA1-80+/SSEA3+ (T0) or C-kit+/CXCR4+ (T5) cells.