Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA121641 | ENA |
REPOSITORIES: ENA
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Project description:DNase hypersensitivity using Nimblegen ENCODE arrays (DNase-chip) in primary human trachea epithelia (pHTE), normal human bronchial epithelia (NHBE), Caco2, HT29, human skin fibroblasts, primary human male epididymis. DNase hypersensitivity mapping is used to detect putative regulatory elements of the human genome. We digested chromatin from the above cell types with DNaseI using the DNase-chip protocol devised by Crawford et al. (Nat. Methods, 2006). Briefly, cells are lysed, chromatin is digested with increasing amounts of DNase I, digested ends are blunted in adequetely digested samples, ligated to biotinylated linkers, purified with streptavidin beads, amplified by LM-PCR. As control, randomly sonicated genomic DNA is used. LM-PCR material was labeled and hybridized to hg_17 ENCODE arrays at Nimblegen facility.
2009-11-01 | GSE18735 | GEO
Project description:DNase hypersensitivity using Nimblegen ENCODE arrays (DNase-chip) in primary human trachea epithelia (pHTE), normal human bronchial epithelia (NHBE), Caco2, HT29, human skin fibroblasts, primary human male epididymis. DNase hypersensitivity mapping is used to detect putative regulatory elements of the human genome. We digested chromatin from the above cell types with DNaseI using the DNase-chip protocol devised by Crawford et al. (Nat. Methods, 2006). Briefly, cells are lysed, chromatin is digested with increasing amounts of DNase I, digested ends are blunted in adequetely digested samples, ligated to biotinylated linkers, purified with streptavidin beads, amplified by LM-PCR. As control, randomly sonicated genomic DNA is used. LM-PCR material was labeled and hybridized to hg_17 ENCODE arrays at Nimblegen facility. DNaseI-digested chromatin was hybridized to Nimblegen ENCODE arrays (build hg17). Randomly sonicated genomic DNA was used as control. Three biological replicates on three arrays were performed for Caco2 cells, three replicates were done with skin fibroblasts (two digestions were pooled and hybridized to a single array [Sample: SkinFibro.sample2]), two replicates on two arrays were performed for pHTE, NHBE, and HT29, and a single experiment for primary male epididymis.
2009-10-31 | E-GEOD-18735 | biostudies-arrayexpress
Project description:DNase hypersensitivity mapping of 3T3 fibroblasts
| PRJNA381864 | ENA
Project description:These samples are being analyzed by the Duke-UNC-Texas-EBI ENCODE consortium. Expression from these cell types will compared to three whole genome open chromatin methodologies: DNaseI hypersensitivity (DNase-seq), Formaldehyde-Assisted Isolation of Regulatory elements (FAIRE-seq), and Chromatin Immunoprecipitation (ChIP-seq) . For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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Project description:ChIP-chip on custom NimbleGen genomic tiling arrays
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Project description:STAT1 ChIP-chip performed on Human Hela S3 Cells for three different platforms. Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts) (5 biological replicates), custom maskless array tiling most of ENCODE with 50mer oligonucleotides end-to-end (3 biological replicates) and custom maskless array tiling most of ENCODE with 36mer oligonucleotides end-to-end (2 biological replicates). The chromatin-immunoprecipitation protocol is the same for all samples, however the labelling and hybridization protocols differ between Nimblegen and custom maskless arrays. Keywords = Transcription Factor Binding, STAT1, ChIP-chip, Human, Genome Tiling Arrays Keywords: other
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Project description:We used NimbleGen Mouse ChIP-chip 3 × 720K RefSeq Promoter Arrays (NimbleGen Roche, Madison, WI). Briefly, we isolated three independent samples of gender and age matched HDAC6KO and WT control CD4+CD25+ Treg, isolated, cross-linked and processed genomic DNA as above. DNA-protein complexes were bound with Foxp3 mAb, and enriched through immunoprecipitation, which a control sample is retained without immunoprecipitation (input). Both input and Foxp3-IP enriched samples underwent whole-genome amplification or ligation mediated-PCR to obtain adequate amounts of DNA for labeling. Foxp3-IP enriched samples were labeled with Cy5, and input samples with Cy3, and the arrays submitted to NimbleGen for analysis. Data were analyzed using Partek GS (Partek Inc., St Louis, MO) and the Broad Institutes Interactive Genome Viewer (Version 2.3.32) (Robinson et al., 2011). Raw data underwent Loess normalization, and Student t-testing with a false discovery rate of 0.1 (p-value cutoff 0.0029). For visualization, we generated IGV files using NimbleGen mapping information from the SignalMap GFF files.
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2006-11-30 | GSE6394 | GEO
Project description:RNA Polymerase II ChIP-chip using monoclonal antibody (8WG16) performed on HeLaS3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Pol II-binding regions. Use of this data requires permission from its producers. Keywords: ChIP-chip
2006-11-30 | GSE6391 | GEO
Project description:NRSF ChIP DNA was isolated from HeLaS3 cells and surveyed for binding in the ENCODE regions on NimbleGen ENCODE arrays. Use of this data requires permission from its producers. Keywords: ChIP-chip
2007-03-28 | GSE7372 | GEO