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  1. Global gene expression kinetics of early human lung development modeled by directed differentiation of human PSCs using an NKX2-1GFP iPSC reporter BioProject

    ID: PRJNA325535

    Access Type: download

  2. Sip1 in cortical interneuron migration BioProject

    ID: PRJNA152545

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: We sequenced mRNA from 6 samples of FACsorted telencephalons from E14.5 Sip1|Nkx2-1 knockout and WT|Nkx2-1 control m...
  3. Suppression of Lung Adenocarcinoma Progression by Nkx2-1 OmicsDI

    ID: E-GEOD-26874

    Date Released: 01-27-2013

    Description: r types. Cross-species analysis identified the NK-2 related homeobox transcription factor Nkx2-1 (Ttf-1/Titf1) as a candidate suppressor of malignant progression. In this mouse model, Nkx2-1-negativity is pathognomonic of high-grade poorly differentiated tumours. Gain- and loss-of-function experiments in cells derived from metastatic and non-metastatic tumours demonstrated that Nkx2-1 controls tumour differentiation and limits metastatic potential in vivo. Interrogation of Nkx2-1 regulated genes, analysis of tumours at defined developmental stages, and functional complementation experiments indicate that Nkx2-1 constrains tumours in part by repressing the embryonically-restricted chromatin regulator Hmga2. While focal amplification of NKX2-1 in a fraction of human lung adenocarcinomas has focused attention on its oncogenic function6-9, our data specifically link Nkx2-1 downregulation to loss of differentiation, enhance...

  4. Nkx2.1 represses a latent gastric differentiation program in lung adenocarcinoma BioProject

    ID: PRJNA153501

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: ams become dysregulated. The transcription factor Nkx2-1 is a master regulator of pulmonary differentiation that is downregulated in poorly differentiated lung adenocarcinoma. Here we use conditional murine genetics to study the fate o...
  5. Nkx2.1 represses a latent gastric differentiation program in lung adenocarcinoma OmicsDI

    ID: E-GEOD-36473

    Date Released: 04-22-2013

    Description: ams become dysregulated. The transcription factor Nkx2-1 is a master regulator of pulmonary differentiation that is downregulated in poorly differentiated lung adenocarcinoma. Here we use conditional murine genetics to study the fate o...

  6. Sip1 in cortical interneuron migration OmicsDI

    ID: E-GEOD-35616

    Date Released: 04-30-2015

    Description: We sequenced mRNA from 6 samples of FACsorted telencephalons from E14.5 Sip1|Nkx2-1 knockout and WT|Nkx2-1 control m...

  7. Nkx2.1 represses a latent gastric differentiation program in lung adenocarcinoma ArrayExpress

    ID: E-GEOD-36473

    Description: ams become dysregulated. The transcription factor Nkx2-1 is a master regulator of pulmonary differentiation that is downregulated in poorly differentiated lung adenocarcinoma. Here we use conditional murine genetics to study the fate o...

  8. Suppression of Lung Adenocarcinoma Progression by Nkx2-1 BioProject

    ID: PRJNA136113

    Keywords: Transcriptome or Gene expression

    Access Type: download

  9. Suppression of Lung Adenocarcinoma Progression by Nkx2-1 ArrayExpress

    ID: E-GEOD-26874

    Description: r types. Cross-species analysis identified the NK-2 related homeobox transcription factor Nkx2-1 (Ttf-1/Titf1) as a candidate suppressor of malignant progression. In this mouse model, Nkx2-1-negativity is pathognomonic of high-grade poorly differentiated tumours. Gain- and loss-of-function experiments in cells derived from metastatic and non-metastatic tumours demonstrated that Nkx2-1 controls tumour differentiation and limits metastatic potential in vivo. Interrogation of Nkx2-1 regulated genes, analysis of tumours at defined developmental stages, and functional complementation experiments indicate that Nkx2-1 constrains tumours in part by repressing the embryonically-restricted chromatin regulator Hmga2. While focal amplification of NKX2-1 in a fraction of human lung adenocarcinomas has focused attention on its oncogenic function6-9, our data specifically link Nkx2-1 downregulation to loss of differentiation, enhance...

  10. Sip1 in cortical interneuron migration ArrayExpress

    ID: E-GEOD-35616

    Description: We sequenced mRNA from 6 samples of FACsorted telencephalons from E14.5 Sip1|Nkx2-1 knockout and WT|Nkx2-1 control m...

  11. Baf250a orchestrates an epigenetic pathway to repress the Nkx2.5-directed contractile cardiomyocyte program in the sinoatrial node BioProject

    ID: PRJNA240540

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: n 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. Overall design: mRNA-seq were performed at 0 hr, 16 hr, 20 hr, 24 hr, 48 hr, and 6 days after tamoxifen treatment....
  12. Transcriptional profiling by array of human cardiac progenitors and cardiomyocytes generated from embryonic bodies, directed differentiation of hESCs ... ArrayExpress

    ID: E-MEXP-3371

    Description: s), we introduced sequences encoding GFP into the NKX2-5 locus by homologous recombination. We found that NKX2-5GFP hESCs facilitate quantification of cardiac differentiation, purification of hESC-derived committed cardiac progenitor cells and cardiomyocytes and the standardization of differentiation protocols....

  13. RNAi knock down in mouse cardiomyocyte cell line HL-1 using siRNAs against Gata4, Mef2a, Nkx2.5 and Srf to identify downstream targets ArrayExpress

    ID: E-TABM-376

    Description: HL-1 cells treated with two different siRNAs against Gata4, Mef2a, Nkx2.5 and Srf each in duplicate to identify downstream targets.

    dataAcquisition.name: Illumina MouseWG-6 v1.1 Expression BeadChip
  14. Baf250a orchestrates an epigenetic pathway to repress the Nkx2.5-directed contractile cardiomyocyte program in the sinoatrial node ArrayExpress

    ID: E-GEOD-55682

    Description: n 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. mRNA-seq were performed at 0 hr, 16 hr, 20 hr, 24 hr, 48 hr, and 6 days after tamoxifen treatment....

  15. Transcription profiling of mouse embryonic stem cells to identify novel cardiac genes through differentiation ArrayExpress

    ID: E-GEOD-10970

    Description: mESCs, using a transgenic mESC line harboring an Nkx2-5 cardiac-specific regulatory sequence driving green fluorescent protein (GFP) to facilitate selection of CPCs. Approximately 24% (43/176) of the transcripts enriched in the CPC population have known roles in cardiac function or development. Importantly, we evaluated the biological relevance of a subset 31/133 (23%) of the remaining candidate genes by in situ hybridization and report that all were expressed in key cardiac structures during cardiogenesis (embryonic day, E7.5 - 9.5), many of which were previously uncharacterized. These data demonstrate the power of mESC differentiation to model specific developmental processes and provide a valuable resource that may be mined to further elucidate the genetic programs underlying cardiogenesis. Exper...

  16. Efficient Array-based Identification of Novel Cardiac Genes through Differentiation of Mouse ESCs BioProject

    ID: PRJNA107169

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: mESCs, using a transgenic mESC line harboring an Nkx2-5 cardiac-specific regulatory sequence driving green fluorescent protein (GFP) to facilitate selection of CPCs. Approximately 24% (43/176) of the transcripts enriched in the CPC population have known roles in cardiac function or development. Importantly, we evaluated the biological relevance of a subset 31/133 (23%) of the remaining candidate genes by in situ hybridization and report that all were expressed in key cardiac structures during cardiogenesis (embryonic day, E7.5 - 9.5), many of which were previously uncharacterized. These data demonstrate the power of mESC differentiation to model specific developmental processes and provide a valuable resource that may be mined to further elucidate the genetic programs underlying cardiogenesis. Keyw...
  17. CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN COMPLEXED WITH BCH-10556 AND EXOSITE-DIRECTED PEPTIDE PDB

    ID: PDB:1G37

    Description: ALPHA THROMBIN (E.C.3.4.21.5), NONAPEPTIDE INHIBITOR

    material.name: 3-(4-AMINO-CYCLOHEXYL)-2-HYDROXY-3-[(4-OXO-2-PHENYLMETHANESULFONYL-1,2,3,4-TETRAHYDRO-PYRROLO[1,2-A]PYRAZINE-6-CARBO...
  18. Transcription profiling of mouse embryonic stem cells to identify novel cardiac genes through differentiation OmicsDI

    ID: E-GEOD-10970

    Date Released: 06-10-2011

    Description: mESCs, using a transgenic mESC line harboring an Nkx2-5 cardiac-specific regulatory sequence driving green fluorescent protein (GFP) to facilitate selection of CPCs. Approximately 24% (43/176) of the transcripts enriched in the CPC population have known roles in cardiac function or development. Importantly, we evaluated the biological relevance of a subset 31/133 (23%) of the remaining candidate genes by in situ hybridization and report that all were expressed in key cardiac structures during cardiogenesis (embryonic day, E7.5 - 9.5), many of which were previously uncharacterized. These data demonstrate the power of mESC differentiation to model specific developmental processes and provide a valuable resource that may be mined to further elucidate the genetic programs underlying cardiogenesis. Exper...

  19. Rewiring of human lung cell lineage and mitotic networks in lung adenocarcinomas ArrayExpress

    ID: E-GEOD-32665

    Description: ated with particular cell lineages (alveolar type 2 pneumocytes and Clara cells) in normal lung and document the changes in these networks that accompany transformation to adenocarcinomas. Expression of the transcription factor NKX2-1 (TTF1) is linked to surfactant protein markers of the alveolar type 2 lineage in normal and transformed lung cells, but its network is rewired in tumors to include pathways linked to cell growth such as glutaminase (GLS2). Analysis of mitotic networks revealed the presence of novel components such as the kinase VRK1 that are preferentially linked to the mitotic cycle in tumors but not in normal lung. We show that shRNA-mediated inhibition of VRK1 cooperates with inhibition of PARP signaling to inhibit growth of lung tumor cells....

  20. Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer: aCGH Arrays ArrayExpress

    ID: E-GEOD-10025

    Description: est region of recurrent amplification spanned the homeobox transcription factor TITF1 (also known as NKX2-1), previously linked to normal lung development and function. When amplified, TITF1 exhibited increased expression at both the RNA and protein level. siRNA-mediated knockdown of TITF1 in lung cancer cell lines with amplification led to reduced cell proliferation, manifested by both decreased cell-cycle progression and increased apoptosis. Our findings...

  21. RNAseq analysis of the colon of intestine-specific adult Nkx2.2 mutant mice ArrayExpress

    ID: E-GEOD-78902

    Description: llin-Cre (Nkx2.2int) mice versus control Methods: 2 cm of the colon (as measured after the caecum) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the...

  22. RNAseq analysis of the duodenum of intestine-specific adult Nkx2.2 mutant mice ArrayExpress

    ID: E-GEOD-72761

    Description: llin-Cre (Nkx2.2int) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the...

  23. Comparative global transcriptomic profiling of human ES and iPSs cells and their derived microdissected cardiac clusters ArrayExpress

    ID: E-GEOD-17579

    Description: S cells (1) and undifferentiated human iPS cells (2), human ES cell-derived cardiomyocytes (3) and human iPS cell-derived cardiomyocytes (4) enriched by microdissection of spontaneously contracting embryoid body outgrowths, and human fetal (5) and adult (6) heart tissue. Total RNA samples were prepared from three independent biological replicates in groups 1-4. In groups 5 and 6, single RNA probes were analyzed as three technical replicates....

  24. RNAseq analysis of the duodenum of intestine-specific adult TN mutant mice BioProject

    ID: PRJNA295013

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: N;Villin-Cre (TNint) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) wi...
  25. RNAseq analysis of the colon of intestine-specific adult Nkx2.2 mutant mice BioProject

    ID: PRJNA314335

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: llin-Cre (Nkx2.2int) mice versus control Methods: 2 cm of the colon (as measured after the caecum) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the...
  26. RNAseq analysis of the duodenum of intestine-specific adult SD mutant mice BioProject

    ID: PRJNA295014

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: D;Villin-Cre (SDint) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) wi...
  27. RNAseq analysis of the duodenum of intestine-specific adult Nkx2.2 mutant mice BioProject

    ID: PRJNA295015

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: llin-Cre (Nkx2.2int) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the...
  28. Lung cancer signatures in plasma based on proteome profiling of mouse tumor models ArrayExpress

    ID: E-GEOD-28480

    Description: nflammation. A set of proteins regulated by Titf1/Nkx2-1, a master transcription factor in cells from the peripheral airways and a known lineage-survival oncogene in lung cancer was identified in plasmas of mouse models of lung adenocarcinoma. An EGFR network of proteins was discerned in the plasma of mice with lung tumors driven by a mutant human EGFR. Levels of these proteins returned toward baseline upon treatment with a tyrosine kinase inhibitor. Moreover, a distinct plasma signature was uncovered in the Trp53/Rb mutant small cell lung cancer model that included a set of proteins associated with neuroendocrine development. Our studies have identified novel plasma protein signatures among molecularly or histopathologically defined lung cancer subtypes. siRNA transfection experiments were performed in NCI-H3255 and HCC4019 lung adenocarcinoma cell lines using ON-TARGETplus SMARTpool small interfering RNAs (siRNAs) targeting TITF1 (L-0191...

  29. Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer: aCGH Arrays BioProject

    ID: PRJNA108579

    Keywords: Variation

    Access Type: download

    dataset.description: est region of recurrent amplification spanned the homeobox transcription factor TITF1 (also known as NKX2-1), previously linked to normal lung development and function. When amplified, TITF1 exhibited increased expression at both the RNA and protein level. siRNA-mediated knockdown of TITF1 in lung cancer cell lines with amplification led to reduced cell proliferation, manifested by both decreased cell-cycle progression and increased apoptosis. Our findings...
  30. RNAseq analysis of the duodenum of intestine-specific adult TN mutant mice ArrayExpress

    ID: E-GEOD-72764

    Description: N;Villin-Cre (TNint) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) wi...

  31. Growth arrest of human thyroid cancer cells 8505C after inhibition of TTF-1 transcriptional activity ArrayExpress

    ID: E-GEOD-58587

    Description: Background: thyroid transcription factor-1 (TTF-1) is known to play key roles in thyroid organogenesis, in thyroid cell proliferation and in the expre...

  32. Growth arrest of human thyroid cancer cells 8505C after inhibition of TTF-1 transcriptional activity ArrayExpress

    ID: E-GEOD-58243

    Description: Background: thyroid transcription factor-1 (TTF-1) is known to play key roles in thyroid organogenesis, in thyroid cell proliferation and in the expre...

  33. Gene transcription, metabolite and lipid profiling in eco-indicator daphnia magna indicate diverse mechanisms of toxicity by legacy and emerging flame... ArrayExpress

    ID: E-GEOD-74736

    Description: emaster 550 (FM550), Firemaster BZ-54 (BZ54), bis(2-ethylhexyl) tetrabromophthalate (BEH-TEBP), triphenyl phosphate (TPhP), and nonbrominated BEH-TEBP analog bis(2-ethylhexyl) phthalate (BEHP) ranged from 0.058 mg/L (pentaBDE) to 3.96 mg/L (octaBDE). mRNA expression, (1)H NMR-based metabolomic and lipidomic profiling at 1/10 LC50 revealed distinct patterns of molecular response for each exposure, suggesting pentaPBDE affects transcription and translation, octaBDE and BEH-TEBP affect glycosphingolipid biosynthesis and BZ54 affects Wnt and Hedgehog signal pathways as well as glycosaminoglycan degradation. Brominated component...

  34. RNAseq analysis of the duodenum of intestine-specific adult SD mutant mice ArrayExpress

    ID: E-GEOD-72762

    Description: D;Villin-Cre (SDint) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) wi...

  35. Comparative global transcriptomic profiling of human ES and iPSs cells and their derived microdissected cardiac clusters BioProject

    ID: PRJNA118681

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: S cells (1) and undifferentiated human iPS cells (2), human ES cell-derived cardiomyocytes (3) and human iPS cell-derived cardiomyocytes (4) enriched by microdissection of spontaneously contracting embryoid body outgrowths, and human fetal (5) and adult (6) heart tissue. Total RNA samples were prepared from three independent biological replicates in groups 1-4. In groups 5 and 6, single RNA probes were analyzed as three technical replicates....
  36. Lung cancer signatures in plasma based on proteome profiling of mouse tumor models BioProject

    ID: PRJNA139309

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: nflammation. A set of proteins regulated by Titf1/Nkx2-1, a master transcription factor in cells from the peripheral airways and a known lineage-survival oncogene in lung cancer was identified in plasmas of mouse models of lung adenocarcinoma. An EGFR network of proteins was discerned in the plasma of mice with lung tumors driven by a mutant human EGFR. Levels of these proteins returned toward baseline upon treatment with a tyrosine kinase inhibitor. Moreover, a distinct plasma signature was uncovered in the Trp53/Rb mutant small cell lung cancer model that included a set of proteins associated with neuroendocrine development. Our studies have identified novel plasma protein signatures among molecularly or histopathologically defined lung cancer subtypes. Overall design: siRNA transfection experiments were performed in NCI-H3255 and HCC4019 lung adenocarcinoma cell lines using ON-TARGETplus SMARTpool small interfering RNAs (siRNAs) targeti...
  37. Transcription profiling of human NSCLC tumor progression ArrayExpress

    ID: E-GEOD-7880

    Description: To identify genes associated with lung cancer progression, we examined gene expression profiles of tumor cells from 20 patients with primary, untreate...

  38. Transcription profiling by array of mouse lumbar spinal cord mutant for tenascin-C ArrayExpress

    ID: E-GEOD-33091

    Description: thermore, we could demonstrate an upregulation of Nk2 transcription factor related locus 2 (Nkx2.2) and its downstream target Sulfatase 1 in vivo. A dorsal expansion of Nkx2.2-positive cells within the ventral spinal cord indicates a potential progenitor cell domain shift. Moreover, Sulfatase 1 is known to regulate growth factor signalling by cleaving sulphate residues from heparan sulphate proteoglycans. Consistent with this possibility we observed changes in both Fibroblast growth factor 2 and Epidermal growth factor responsiveness of spinal cord neural precursor cells. Taken together our data clearly show that Tenascin-C promotes the astroglial lineage prog...

  39. Gene transcription, metabolite and lipid profiling in eco-indicator daphnia magna indicate diverse mechanisms of toxicity by legacy and emerging flame... BioProject

    ID: PRJNA301365

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: emaster 550 (FM550), Firemaster BZ-54 (BZ54), bis(2-ethylhexyl) tetrabromophthalate (BEH-TEBP), triphenyl phosphate (TPhP), and nonbrominated BEH-TEBP analog bis(2-ethylhexyl) phthalate (BEHP) ranged from 0.058 mg/L (pentaBDE) to 3.96 mg/L (octaBDE). mRNA expression, (1)H NMR-based metabolomic and lipidomic profiling at 1/10 LC50 revealed distinct patterns of molecular response for each exposure, suggesting pentaPBDE affects transcription and translation, octaBDE and BEH-TEBP affect glycosphingolipid biosynthesis and BZ54 affects Wnt and Hedgehog signal pathways as well as glycosaminoglycan degradation. Brominated component...
  40. Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer: aCGH Arrays OmicsDI

    ID: E-GEOD-10025

    Date Released: 05-01-2014

    Description: est region of recurrent amplification spanned the homeobox transcription factor TITF1 (also known as NKX2-1), previously linked to normal lung development and function. When amplified, TITF1 exhibited increased expression at both the RNA and protein level. siRNA-mediated knockdown of TITF1 in lung cancer cell lines with amplification led to reduced cell proliferation, manifested by both decreased cell-cycle progression and increased apoptosis. Our findings...

  41. Impact of cytosine methylation on DNA binding specificities of human transcription factors. BioProject

    ID: PRJNA371642

    Keywords: Other

    Access Type: download

    dataset.description: described in Mann et al., Genome Res. 2013 Jun;23(6):988-97....
  42. Growth arrest of human thyroid cancer cells 8505C after inhibition of TTF-1 transcriptional activity BioProject

    ID: PRJNA251721

    Keywords: Transcriptome or Gene expression

    Access Type: download

  43. Growth arrest of human thyroid cancer cells 8505C after inhibition of TTF-1 transcriptional activity BioProject

    ID: PRJNA252940

    Keywords: Transcriptome or Gene expression

    Access Type: download

  44. Molecular profiling of tumor progression in NSCLC GEMMA

    ID: 556

    Keywords: functional genomics

    Description: To identify genes associated with lung cancer progression, we examined gene expression profiles of tumor cells from 20 patients with primary, untreate...

  45. Tenascin-C modifies expression levels and territories of key patterning genes during spinal cord astrocyte specification [mus musculus] BioProject

    ID: PRJNA149343

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: thermore, we could demonstrate an upregulation of Nk2 transcription factor related locus 2 (Nkx2.2) and its downstream target Sulfatase 1 in vivo. A dorsal expansion of Nkx2.2-positive cells within the ventral spinal cord indicates a potential progenitor cell domain shift. Moreover, Sulfatase 1 is known to regulate growth factor signalling by cleaving sulphate residues from heparan sulphate proteoglycans. Consistent with this possibility we observed changes in both Fibroblast growth factor 2 and Epidermal growth factor responsiveness of spinal cord neural precursor cells. Taken together our data clearly show that Tenascin-C promotes the astroglial lineage prog...
  46. Molecular profiling of tumor progression in NSCLC BioProject

    ID: PRJNA99911

    Keywords: Transcriptome or Gene expression

    Access Type: download

  47. Lung cancer signatures in plasma based on proteome profiling of mouse tumor models OmicsDI

    ID: E-GEOD-28480

    Date Released: 06-02-2014

    Description: nflammation. A set of proteins regulated by Titf1/Nkx2-1, a master transcription factor in cells from the peripheral airways and a known lineage-survival oncogene in lung cancer was identified in plasmas of mouse models of lung adenocarcinoma. An EGFR network of proteins was discerned in the plasma of mice with lung tumors driven by a mutant human EGFR. Levels of these proteins returned toward baseline upon treatment with a tyrosine kinase inhibitor. Moreover, a distinct plasma signature was uncovered in the Trp53/Rb mutant small cell lung cancer model that included a set of proteins associated with neuroendocrine development. Our studies have identified novel plasma protein signatures among molecularly or histopathologically defined lung cancer subtypes. siRNA transfection experiments were performed in NCI-H3255 and HCC4019 lung adenocarcinoma cell lines using ON-TARGETplus SMARTpool small interfering RNAs (siRNAs) targeting TITF1 (L-0191...

  48. Cardiac differentiation of embryonic stem cells recapitulates embryonic cardiac development. BioProject

    ID: PRJNA96951

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: /ml) and it was exchanged with fresh medium every 2 days during differentiation. Transfection of mouse embryonic stem cells The mouse Nkx2.5 enhancer fragment #5(Lien et al., 1999) and the hsp68 minimal promoter was excised from the provided vector (XhoI/ NcoI) and inserted in front of the EGFP gene in the Bluescript vector. A vector containing the hygromycin resistance gene (hygromycin phosphotransferase) under the control of the mouse polymerase II promoter was also used in order to select for the transfected mESCs. Prior to transfection the two vectors were linearized. Undifferentiated mESCs were grown to confluency on a layer of primary embryonic fibroblasts and dissociated with trypsin. The cells were combined with the linearized DNA and electroporated (Biorad Gene Pulser Xcell, 240V/ 500?F). The cells were then replated on a fresh layer of PMEFs. Hygromycin B (Invitrogen, cat.# 10687-010, 50?g/ml) was used for 7 days after transfection for selection. Resistant colonies were picked and grown on layers of PMEFs in the presence of antibiotic. Once sufficient cells were present the clones were differentiated in order to check for the correct expression of the GFP in the cardiac areas (spontaneously contracting) of the differentiating cultures. Successful clones were further amplified and used for characterization of the GFP expressing cardiac progenitor cells. In order to select mESC derived cardiomyocytes for the microarray analysis experiment, a stable transgenic clone of mESCs was made that allowed the expression of the neomycin resistance gene under the control of the alpha myosin heavy chain promoter (U71441) as described by Klug et al., (Klug et al., 1996). The transgenic clone was prepared as described above. FACS Analysis For determination of the CPC yield in the differentiating cells, EBs were harvested at the indicated timepoints (between days 6 and 10 of differentiation). Each sample contained approximately 100 hanging droplets on day 0 of differentiation. The EBs were washed in PBS and resuspended in 0.05% trypsin at 4oC (1/2 hour) and 37oC (10 minutes). The percentage of GFP+ cells was determined in a BD FACS Calibur (Cell Quest Pro software). Age matched EBs from untransfected mESCs were used as negative controls. Cells from the same samples were also counted. FACS sorting The BD Biosciences FACSAria Cell sorting system was used to sort the GFP+ and GFP- cells between days 5 and 10 of differentiation. EBs were harvested and dissociated as described above. The cells were suspended in sorting medium (96% DMEM without phenol red, 1% fetal bovine serum, 1% Glutamax, 1% non essential amino acids, 1% sodium pyruvate, 25?g/ml gentamicin) and kept at 4oC. The cells were sorted into a fetal bovine serum rich medium (20%) in order to increase their survival. For further culture the cells were resuspended in mESC culture medium at a concentration of 5x105 cells/ml and cultured in suspension for 48 hours. The cells were then transferred on tissue culture plates for another 48 hours. For RNA isolation the cells were spun down and washed in PBS be...
  49. Transcription profiling of mouse embryonic stem cell line mESC D3 reveals cardiac differentiation of embryonic stem cells recapitulates embryonic card... ArrayExpress

    ID: E-GEOD-5671

    Description: /ml) and it was exchanged with fresh medium every 2 days during differentiation. Experiment Overall Design: Transfection of mouse embryonic stem cells Experiment Overall Design: The mouse Nkx2.5 enhancer fragment #5(Lien et al., 1999) and the hsp68 minimal promoter was excised from the provided vector (XhoI/ NcoI) and inserted in front of the EGFP gene in the Bluescript vector. A vector containing the hygromycin resistance gene (hygromycin phosphotransferase) under the control of the mouse polymerase II promoter was also used in order to select for the transfected mESCs. Prior to transfection the two vectors were linearized. Undifferentiated mESCs were grown to confluency on a layer of primary embryonic fibroblasts and dissociated with trypsin. The cells were combined with the linearized DNA and electroporated (Biorad Gene Pulser Xcell, 240V/ 500?F). The cells were then replated on a fresh layer of PMEFs. Hygromycin B (Invitrogen, cat.# 10687-010, 50?g/ml) was used for 7 days after transfection for selection. Resistant colonies were picked and grown on layers of PMEFs in the presence of antibiotic. Once sufficient cells were present the clones were differentiated in order to check for the correct expression of the GFP in the cardiac areas (spontaneously contracting) of the differentiating cultures. Successful clones were further amplified and used for characterization of the GFP expressing cardiac progenitor cells. Experiment Overall Design: In order to select mESC derived cardiomyocytes for the microarray analysis experiment, a stable transgenic clone of mESCs was made that allowed the expression of the neomycin resistance gene under the control of the alpha myosin heavy chain promoter (U71441) as described by Klug et al., (Klug et al., 1996). The transgenic clone was prepared as described above. Experiment Overall Design: FACS Analysis Experiment Overall Design: For determination of the CPC yield in the differentiating cells, EBs were harvested at the indicated timepoints (between days 6 and 10 of differentiation). Each sample contained approximately 100 hanging droplets on day 0 of differentiation. The EBs were washed in PBS and resuspended in 0.05% trypsin at 4oC (1/2 hour) and 37oC (10 minutes). The percentage of GFP+ cells was determined in a BD FACS Calibur (Cell Quest Pro software). Age matched EBs from untransfected mESCs were used as negative controls. Cells from the same samples were also counted. Experiment Overall Design: FACS sorting Experiment Overall Design: The BD Biosciences FACSAria Cell sorting system was used to sort the GFP+ and GFP- cells between days 5 and 10 of differentiation. EBs were harvested and dissociated as described above. The cells were suspended in sorting medium (96% DMEM without phenol red, 1% fetal bovine serum, 1% Glutamax, 1% non essential amino acids, 1% sodium pyruvate, 25?g/ml gentamicin) and kept at 4oC. The cells were sorted into a fetal bovine serum rich medium (20%) in order to increase their survival. For further culture the cells were resuspended in m...

  50. eMERGE Network Imputed GWAS for 41 phenotypes dbGaP

    ID: phs000888.v1.p1

    Description: c Kidney Disease; Chronic Kidney Disease and Type 2 Diabetes; Chronic Kidney Disease, Type 2 Diabetes and Hypertension; Colon Polyps; Cardiorespiratory Fitness; Dementia; Diverticulosis; Diabetic retinopathy; Gastroesophageal Reflux Disease; Glaucoma; Height; Heart failure; Hypothyroidism; Lipids; Ocular hypertension; Peripheral Arterial Disease; QRS duration; Red blood cell indices; Remission of Diabetes after ROUX-EN-Y gastric bypass surgery; Resistant hypertension; MACE while on Statins; Type 2 Diabetes; Venous Thromboembolism; White blood cell indices; and Zoster virus infection, as well as using the phenome-wide association study (PheWAS) paradigm to replicate and discover relationships between targeted genotypes with multiple phenotypes. Sites and participants include: Children's Hospital of Pennsylvania (CHOP): The Center for Applied Genomics (CAG) at the Children's Hospital of Philadelphia (CHOP) is a high-throughput, highly automated genotyping and sequencing facility equipped with state-of-the-art genotyping and sequencing platforms. Children who are treated at the Children's Hospital Healthcare Network and their parents may be eligible to take part in a major initiative to collect more than 100,000 blood samples, covering a wide range of pediatric diseases. A large majority of participants consenting to prospective genomic analyses also consent to analysis of their de-identified electro...


Displaying 50 of 52 results for "NKX2-6"