Identification of lipid-binding lncRNAs in triple-negative breast cancer
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE92414 | GEO | 2017/02/21
SECONDARY ACCESSION(S): PRJNA357495
REPOSITORIES: GEO
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Project description:We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80mM or 150mM NaCl after digestion contain predominantly mononucleosomes and represent calssical 'active' chromatin. Profiles of these low-salt-soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of RNA polymerase II. Nearly quantitative recovery of chromatin is obtained with 600mM NaCl, however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics. Keywords: Chromatin affinity-purification on microarray For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf All experiments were done using two channels per chip, comparing DNAs extracted from either salt-extracted or insoluble chromatin to whole nuclear chromatin, whole nuclear chromatin to randomly fragmented genomic DNA, streptavidin-bound biotin-tagged histone-variant-containing chromatin to salt-extracted chromatin, gel-purified mononucleosomes to whole EDTA-extracted soluble chromatin, streptavidin-bound biotin-tagged histone-variant-containing chromatin to whole EDTA-extracted soluble chromatin, or oligo(dT)-primed cDNA to randomly fragmented genomic DNA from S2 cell nuclei.
2008-12-11 | E-GEOD-13217 | biostudies-arrayexpress
Project description:To identify novel TNBC-relevant lncRNAs, we performed lncRNA microarray analysis using 5 TNBC tissues and their matched adjacent non-cancerous tissues by Arraystar Human LncRNA Microarray V3.0.
2021-07-01 | GSE156144 | GEO
Project description:We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80mM or 150mM NaCl after digestion contain predominantly mononucleosomes and represent calssical 'active' chromatin. Profiles of these low-salt-soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of RNA polymerase II. Nearly quantitative recovery of chromatin is obtained with 600mM NaCl, however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics. Keywords: Chromatin affinity-purification on microarray For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2008-12-12 | GSE13217 | GEO
Project description:Initial insoluble fractions on K562 Long Total from Lecuyer For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2016-11-08 | GSE88473 | GEO
Project description:Initial insoluble fractions on K562 Long Poly-A+ from Lecuyer For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2016-11-08 | GSE88383 | GEO
Project description:Initial insoluble cytoplasmic fractions on HepG2 Long Total from Lecuyer For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2016-11-08 | GSE88561 | GEO
Project description:Initial insoluble fractions on HepG2 Long Poly-A+ from Lecuyer For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2016-11-08 | GSE87958 | GEO
Project description:We looked for the presence of prostatic cells and RNAs (cellular and acellular) of prostatic origin in the ejaculate semen from fertile and sterilized men and from men with prostate cancer, to ascertain the suitability of ejaculate semen for studying and monitoring prostate health. Methods. For prostatic cells, semen from fertile and sterile men and men with prostate cancer were subjected to density gradient centrifugation on a 60% cushion of Suprasperm™ and fractions containing somatic cells were washed and cytospun onto coated slides prior to fixation and immunocytochemistry with antibodies recognizing prostatic markers. Small RNAs were isolated from liquefied semen clarified of all cellular and other insoluble material by high-speed ultra-centrifugation. Sequencing libraries were prepared from fractions isolated by PAGE, corresponding to small non-coding (snc) RNAs in the 18-23 nt and 30-35 nt size ranges. Libraries were interrogated by next generation sequencing and analysed to generate lists of differentially expressed RNAs associated with cancer and sterility. Results. Cells positive for cytokeratin 18, PSMA, NKX3.1 and CD24 were observed in most ejaculate samples by indirect immunocytochemistry as either discrete cellular entities or within clumps of cell containing material (DAPI+; antigen positive and negative) and cytoplasmic fragments (DAP–; antigen positive and negative). RNA from populations of cells enriched by differential density gradient centrifugation supported their immunocytochemical designation as prostatic cells. Small RNAs (18 - 43 nt) from seminal plasma were highly heterogeneous although tRNAs and 5SRNAs were the dominant forms. A degree of overlap between the respective differential expression profiles of small RNAs from sterile and cancer samples, suggested a common feature, perhaps indicating an inflammatory response. Conclusion. This study supports a wider appraisal of ejaculate semen for studying and monitoring prostate health.
2020-03-31 | GSE117968 | GEO
Project description:modENCODE_submission_2757 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes. Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2010-11-18 | GSE25386 | GEO
Project description:modENCODE_submission_2756 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes. Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2010-11-18 | GSE25385 | GEO