Comprehensive multi-mark and multi-omic profiling reveals epigenetic and transcriptional reprogramming in lung tumors
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE230932 | GEO | 2024/05/31
REPOSITORIES: GEO
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Project description:Transposable elements (TE) have been shown to contrain functional transcription factor (TF) binding sites for long, but the extent to which TEs contribute TF binding sites is not well know. Here, we comprehensively mapped binding sites for 26 pairs of orthologous TFs, in two pairs of human and mouse cell lines (i.e., leukemia, and lymphoblast), along with epigenomic profiles representing DNA methylation and six histone modifications. We found that on average, 20% of TF binding sites were embedded in TEs. We further identified 710 TF-TE relationships in which certain TE subfamilies enriched for TF binidng sites. TE-derived TF binding peaks were also strongly associated with decreased DNA methylation and increased enhancer-associated histone marks. Most of the TE-derived TF binding sites were species-specific, but we also identified conserved binding sites. Additionally, 66% of TE-derived TF binding events were cell-type specific, associated with cell-type specific epigenetic landscape. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf To evaluate the contribution of transposable elements (TE) to transcription factor (TF) binding landscapes, we profiled ChIP-seq datasets for 26 TFs in two cell lines in human and mouse, generated by the ENCODE and MouseENCODE consortia. The epigenomic profiles were evaluated from six histone modification in each of the cell lines, also generated by the consortia. We added DNA methylation to the epigenomic profiles, using two complementary techniques, MeDIP-seq and MRE-seq. The mouse data related to this study are available through GSE57230: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57230
2014-05-09 | E-GEOD-56774 | biostudies-arrayexpress
Project description:Transposable elements (TE) have been shown to contrain functional transcription factor (TF) binding sites for long, but the extent to which TEs contribute TF binding sites is not well know. Here, we comprehensively mapped binding sites for 26 pairs of orthologous TFs, in two pairs of human and mouse cell lines (i.e., leukemia, and lymphoblast), along with epigenomic profiles representing DNA methylation and six histone modifications. We found that on average, 20% of TF binding sites were embedded in TEs. We further identified 710 TF-TE relationships in which certain TE subfamilies enriched for TF binidng sites. TE-derived TF binding peaks were also strongly associated with decreased DNA methylation and increased enhancer-associated histone marks. Most of the TE-derived TF binding sites were species-specific, but we also identified conserved binding sites. Additionally, 66% of TE-derived TF binding events were cell-type specific, associated with cell-type specific epigenetic landscape. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf To evaluate the contribution of transposable elements (TE) to transcription factor (TF) binding landscapes, we profiled ChIP-seq datasets for 26 TFs in two cell lines in human and mouse, generated by the ENCODE and MouseENCODE consortia. The epigenomic profiles were evaluated from six histone modification in each of the cell lines, also generated by the consortia. We added DNA methylation to the epigenomic profiles, using two complementary techniques, MeDIP-seq and MRE-seq. The human data related to this study are available through GSE56774: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56774
2014-05-09 | E-GEOD-57230 | biostudies-arrayexpress
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2012-02-08 | GSE35614 | GEO
Project description:The study demonstrated the gene expression through microarray analysis of total mRNA in rams experimentally infected with a rough (R) virulent strain of Brucella ovis in reproductive organs (epididymus, testicles, ampolae, vesicular glands, bulbourethral glands) and a pool of lymph nodes (inguinal and scrotal) at three different times: acute phase (60 days post challenge [dpc]), chronic phase 1 (120dpc), and chronic phase 2 (240dpc) of infection. To further define the gene expression changes associated with infected rams, the profiles of a control group (0 dpc) of rams was compared using the Affymetrix Bovine Genome Array. Of the 23,000 genes that were analyzed on the array, B. ovis infection in rams’ tissues revealed 139, 930 and 744 Differentially Expressed Genes (DEGs) in the acute, chronic 1, and chronic phase 2 of infection, respectively. Among the three phases of infection, 44 DEGs (30 known and 14 unknown genes) were expressed in common. The biological functions of immune cell trafficking, immunological disease, infectious disease, inflammatory disease, inflammatory response and cellular movement were significant at the three phases of infection. The results support the first microarray analysis of ram tissues infected with an R strain of B. ovis.
2012-02-08 | GSE35613 | GEO
Project description:The study demonstrated the gene expression through microarray analysis of total mRNA in rams experimentally infected with a rough (R) virulent strain of Brucella ovis in reproductive organs (epididymus, testicles, ampolae, vesicular glands, bulbourethral glands) and a pool of lymph nodes (inguinal and scrotal) at three different times: acute phase (60 days post challenge [dpc]), chronic phase 1 (120dpc), and chronic phase 2 (240dpc) of infection. To further define the gene expression changes associated with infected rams, the profiles of a control group (0 dpc) of rams was compared using the Affymetrix Bovine Genome Array. Of the 23,000 genes that were analyzed on the array, B. ovis infection in rams’ tissues revealed 139, 930 and 744 Differentially Expressed Genes (DEGs) in the acute, chronic 1, and chronic phase 2 of infection, respectively. Among the three phases of infection, 44 DEGs (30 known and 14 unknown genes) were expressed in common. The biological functions of immune cell trafficking, immunological disease, infectious disease, inflammatory disease, inflammatory response and cellular movement were significant at the three phases of infection. The results support the first microarray analysis of ram tissues infected with an R strain of B. ovis.
2012-02-08 | GSE35612 | GEO
Project description:The study demonstrated the gene expression through microarray analysis of total mRNA in rams experimentally infected with a rough (R) virulent strain of Brucella ovis in reproductive organs (epididymus, testicles, ampolae, vesicular glands, bulbourethral glands) and a pool of lymph nodes (inguinal and scrotal) at three different times: acute phase (60 days post challenge [dpc]), chronic phase 1 (120dpc), and chronic phase 2 (240dpc) of infection. To further define the gene expression changes associated with infected rams, the profiles of a control group (0 dpc) of rams was compared using the Affymetrix Bovine Genome Array. Of the 23,000 genes that were analyzed on the array, B. ovis infection in rams’ tissues revealed 139, 930 and 744 Differentially Expressed Genes (DEGs) in the acute, chronic 1, and chronic phase 2 of infection, respectively. Among the three phases of infection, 44 DEGs (30 known and 14 unknown genes) were expressed in common. The biological functions of immune cell trafficking, immunological disease, infectious disease, inflammatory disease, inflammatory response and cellular movement were significant at the three phases of infection. The results support the first microarray analysis of ram tissues infected with an R strain of B. ovis. A total of twelve 12-month-old healthy Santa Inês rams, previously diagnosed as negative for brucellosis/visna maedi/toxoplasmosis/neosporosis, were selected for the study. The rams were kept in an isolated pen and experimentally challenged with a rough (R) virulent B. ovis PA strain (ATCC 25840). For the experiment, the rams were classified during the course of infection according to time: 0 dpc (control), 60 dpc (acute phase), 120 dpc (chronic phase 1) and 240 dpc (chronic phase 2). For each time, the tissues epididymus, testicles, ampolae, vesicular glands, bulbourethral glands, and a pool of lymph nodes (inguinal and scrotal) were collected. Three rams were euthanized and necropsied for tissues collection purposes for each time. To define the gene expression changes associated with infected rams, the profile of a control group (0 dpc) of rams was compared using microarray technology. REPLACE This dataset includes control samples and acute phase samples.
2012-02-08 | E-GEOD-35612 | biostudies-arrayexpress
Project description:The study demonstrated the gene expression through microarray analysis of total mRNA in rams experimentally infected with a rough (R) virulent strain of Brucella ovis in reproductive organs (epididymus, testicles, ampolae, vesicular glands, bulbourethral glands) and a pool of lymph nodes (inguinal and scrotal) at three different times: acute phase (60 days post challenge [dpc]), chronic phase 1 (120dpc), and chronic phase 2 (240dpc) of infection. To further define the gene expression changes associated with infected rams, the profiles of a control group (0 dpc) of rams was compared using the Affymetrix Bovine Genome Array. Of the 23,000 genes that were analyzed on the array, B. ovis infection in rams’ tissues revealed 139, 930 and 744 Differentially Expressed Genes (DEGs) in the acute, chronic 1, and chronic phase 2 of infection, respectively. Among the three phases of infection, 44 DEGs (30 known and 14 unknown genes) were expressed in common. The biological functions of immune cell trafficking, immunological disease, infectious disease, inflammatory disease, inflammatory response and cellular movement were significant at the three phases of infection. The results support the first microarray analysis of ram tissues infected with an R strain of B. ovis. A total of twelve 12-month-old healthy Santa Inês rams, previously diagnosed as negative for brucellosis/visna maedi/toxoplasmosis/neosporosis, were selected for the study. The rams were kept in an isolated pen and experimentally challenged with a rough (R) virulent B. ovis PA strain (ATCC 25840). For the experiment, the rams were classified during the course of infection according to time: 0 dpc (control), 60 dpc (acute phase), 120 dpc (chronic phase 1) and 240 dpc (chronic phase 2). For each time, the tissues epididymus, testicles, ampolae, vesicular glands, bulbourethral glands, and a pool of lymph nodes (inguinal and scrotal) were collected. Three rams were euthanized and necropsied for tissues collection purposes for each time. To define the gene expression changes associated with infected rams, the profile of a control group (0 dpc) of rams was compared using microarray technology. REPLACE This dataset includes control samples and chronic 1 phase samples.
2012-02-08 | E-GEOD-35613 | biostudies-arrayexpress
Project description:The study demonstrated the gene expression through microarray analysis of total mRNA in rams experimentally infected with a rough (R) virulent strain of Brucella ovis in reproductive organs (epididymus, testicles, ampolae, vesicular glands, bulbourethral glands) and a pool of lymph nodes (inguinal and scrotal) at three different times: acute phase (60 days post challenge [dpc]), chronic phase 1 (120dpc), and chronic phase 2 (240dpc) of infection. To further define the gene expression changes associated with infected rams, the profiles of a control group (0 dpc) of rams was compared using the Affymetrix Bovine Genome Array. Of the 23,000 genes that were analyzed on the array, B. ovis infection in rams’ tissues revealed 139, 930 and 744 Differentially Expressed Genes (DEGs) in the acute, chronic 1, and chronic phase 2 of infection, respectively. Among the three phases of infection, 44 DEGs (30 known and 14 unknown genes) were expressed in common. The biological functions of immune cell trafficking, immunological disease, infectious disease, inflammatory disease, inflammatory response and cellular movement were significant at the three phases of infection. The results support the first microarray analysis of ram tissues infected with an R strain of B. ovis. A total of twelve 12-month-old healthy Santa Inês rams, previously diagnosed as negative for brucellosis/visna maedi/toxoplasmosis/neosporosis, were selected for the study. The rams were kept in an isolated pen and experimentally challenged with a rough (R) virulent B. ovis PA strain (ATCC 25840). For the experiment, the rams were classified during the course of infection according to time: 0 dpc (control), 60 dpc (acute phase), 120 dpc (chronic phase 1) and 240 dpc (chronic phase 2). For each time, the tissues epididymus, testicles, ampolae, vesicular glands, bulbourethral glands, and a pool of lymph nodes (inguinal and scrotal) were collected. Three rams were euthanized and necropsied for tissues collection purposes for each time. To define the gene expression changes associated with infected rams, the profile of a control group (0 dpc) of rams was compared using microarray technology. REPLACE This dataset includes control samples and chronic 2 phase samples.
2012-02-08 | E-GEOD-35614 | biostudies-arrayexpress
Project description:Transposable elements (TE) have been shown to contrain functional transcription factor (TF) binding sites for long, but the extent to which TEs contribute TF binding sites is not well know. Here, we comprehensively mapped binding sites for 26 pairs of orthologous TFs, in two pairs of human and mouse cell lines (i.e., leukemia, and lymphoblast), along with epigenomic profiles representing DNA methylation and six histone modifications. We found that on average, 20% of TF binding sites were embedded in TEs. We further identified 710 TF-TE relationships in which certain TE subfamilies enriched for TF binidng sites. TE-derived TF binding peaks were also strongly associated with decreased DNA methylation and increased enhancer-associated histone marks. Most of the TE-derived TF binding sites were species-specific, but we also identified conserved binding sites. Additionally, 66% of TE-derived TF binding events were cell-type specific, associated with cell-type specific epigenetic landscape. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2014-05-09 | GSE57230 | GEO