Chromatin Immunoprecipitation:Article Title: One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase-seq data Yue et al.26,26 GEO: GSE37074 ATAC-seq data Kim et al.25 GEO: GSE113912 Histone ChIP-seq data ENCODE Project Consortium 2012 https://www.encodeproject.org/ WGBS data Lu et al.27 GEO: GSE56986 hMeDIP-seq data Tan et al.38 GEO: GSE40810 TAB-seq data Yu et al.28 GEO: GSM882244 Mx-TOP and RNA-seq data This work GEO: GSE231929 Experimental models: Cell lines E14TG2a, mouse embryonic stem cells American Type Culture Collection (ATCC) Cat# CRL-1821; RRID: CVCL_9108 Oligonucleotides Mx-TOP adapters for Ion Torrent sequencing: A1, 5’-P-GATTGGAAGAGTGGTTCAGCAGGA ATGCTGAG and A2, 5’-ACACTCTTTCCCTAC ATGACACTCTTCCAATCT Metabion N/A 2x-TOP TO (tethered oligonucleotide) for Ion Torrent sequencing: alkyne-TT-biotin-ODN, 50-TXTTTTGTGTGGTTTGGAGACTGACTACC AGATGTAACA-Biotin (X=C8-alkyne-dU) Base-click N/A 3x-TOP TO for Ion Torrent sequencing: amine-TT-biotin-ODN, 5‘-TXTTTTGTGTGGTT TGGA GACTGACTACCAGATGTAACA-Biotin (X = C2-amine-dT). .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase-seq data Yue et al.26,26 GEO: GSE37074 ATAC-seq data Kim et al.25 GEO: GSE113912 Histone ChIP-seq data ENCODE Project Consortium 2012 https://www.encodeproject.org/ WGBS data Lu et al.27 GEO: GSE56986 hMeDIP-seq data Tan et al.38 GEO: GSE40810 TAB-seq data Yu et al.28 GEO: GSM882244 Mx-TOP and RNA-seq data This work GEO: GSE231929 Experimental models: Cell lines E14TG2a, mouse embryonic stem cells American Type Culture Collection (ATCC) Cat# CRL-1821; RRID: CVCL_9108 Oligonucleotides Mx-TOP adapters for Ion Torrent sequencing: A1, 5’-P-GATTGGAAGAGTGGTTCAGCAGGA ATGCTGAG and A2, 5’-ACACTCTTTCCCTAC ATGACACTCTTCCAATCT Metabion N/A 2x-TOP TO (tethered oligonucleotide) for Ion Torrent sequencing: alkyne-TT-biotin-ODN, 50-TXTTTTGTGTGGTTTGGAGACTGACTACC AGATGTAACA-Biotin (X=C8-alkyne-dU) Base-click N/A 3x-TOP TO for Ion Torrent sequencing: amine-TT-biotin-ODN, 5‘-TXTTTTGTGTGGTT TGGA GACTGACTACCAGATGTAACA-Biotin (X = C2-amine-dT).
RNA Sequencing:Article Title: One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase-seq data Yue et al.26,26 GEO: GSE37074 ATAC-seq data Kim et al.25 GEO: GSE113912 Histone ChIP-seq data ENCODE Project Consortium 2012 https://www.encodeproject.org/ WGBS data Lu et al.27 GEO: GSE56986 hMeDIP-seq data Tan et al.38 GEO: GSE40810 TAB-seq data Yu et al.28 GEO: GSM882244 Mx-TOP and RNA-seq data This work GEO: GSE231929 Experimental models: Cell lines E14TG2a, mouse embryonic stem cells American Type Culture Collection (ATCC) Cat# CRL-1821; RRID: CVCL_9108 Oligonucleotides Mx-TOP adapters for Ion Torrent sequencing: A1, 5’-P-GATTGGAAGAGTGGTTCAGCAGGA ATGCTGAG and A2, 5’-ACACTCTTTCCCTAC ATGACACTCTTCCAATCT Metabion N/A 2x-TOP TO (tethered oligonucleotide) for Ion Torrent sequencing: alkyne-TT-biotin-ODN, 50-TXTTTTGTGTGGTTTGGAGACTGACTACC AGATGTAACA-Biotin (X=C8-alkyne-dU) Base-click N/A 3x-TOP TO for Ion Torrent sequencing: amine-TT-biotin-ODN, 5‘-TXTTTTGTGTGGTT TGGA GACTGACTACCAGATGTAACA-Biotin (X = C2-amine-dT). .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase-seq data Yue et al.26,26 GEO: GSE37074 ATAC-seq data Kim et al.25 GEO: GSE113912 Histone ChIP-seq data ENCODE Project Consortium 2012 https://www.encodeproject.org/ WGBS data Lu et al.27 GEO: GSE56986 hMeDIP-seq data Tan et al.38 GEO: GSE40810 TAB-seq data Yu et al.28 GEO: GSM882244 Mx-TOP and RNA-seq data This work GEO: GSE231929 Experimental models: Cell lines E14TG2a, mouse embryonic stem cells American Type Culture Collection (ATCC) Cat# CRL-1821; RRID: CVCL_9108 Oligonucleotides Mx-TOP adapters for Ion Torrent sequencing: A1, 5’-P-GATTGGAAGAGTGGTTCAGCAGGA ATGCTGAG and A2, 5’-ACACTCTTTCCCTAC ATGACACTCTTCCAATCT Metabion N/A 2x-TOP TO (tethered oligonucleotide) for Ion Torrent sequencing: alkyne-TT-biotin-ODN, 50-TXTTTTGTGTGGTTTGGAGACTGACTACC AGATGTAACA-Biotin (X=C8-alkyne-dU) Base-click N/A 3x-TOP TO for Ion Torrent sequencing: amine-TT-biotin-ODN, 5‘-TXTTTTGTGTGGTT TGGA GACTGACTACCAGATGTAACA-Biotin (X = C2-amine-dT).
Sequencing:Article Title: One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase-seq data Yue et al.26,26 GEO: GSE37074 ATAC-seq data Kim et al.25 GEO: GSE113912 Histone ChIP-seq data ENCODE Project Consortium 2012 https://www.encodeproject.org/ WGBS data Lu et al.27 GEO: GSE56986 hMeDIP-seq data Tan et al.38 GEO: GSE40810 TAB-seq data Yu et al.28 GEO: GSM882244 Mx-TOP and RNA-seq data This work GEO: GSE231929 Experimental models: Cell lines E14TG2a, mouse embryonic stem cells American Type Culture Collection (ATCC) Cat# CRL-1821; RRID: CVCL_9108 Oligonucleotides Mx-TOP adapters for Ion Torrent sequencing: A1, 5’-P-GATTGGAAGAGTGGTTCAGCAGGA ATGCTGAG and A2, 5’-ACACTCTTTCCCTAC ATGACACTCTTCCAATCT Metabion N/A 2x-TOP TO (tethered oligonucleotide) for Ion Torrent sequencing: alkyne-TT-biotin-ODN, 50-TXTTTTGTGTGGTTTGGAGACTGACTACC AGATGTAACA-Biotin (X=C8-alkyne-dU) Base-click N/A 3x-TOP TO for Ion Torrent sequencing: amine-TT-biotin-ODN, 5‘-TXTTTTGTGTGGTT TGGA GACTGACTACCAGATGTAACA-Biotin (X = C2-amine-dT). .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase-seq data Yue et al.26,26 GEO: GSE37074 ATAC-seq data Kim et al.25 GEO: GSE113912 Histone ChIP-seq data ENCODE Project Consortium 2012 https://www.encodeproject.org/ WGBS data Lu et al.27 GEO: GSE56986 hMeDIP-seq data Tan et al.38 GEO: GSE40810 TAB-seq data Yu et al.28 GEO: GSM882244 Mx-TOP and RNA-seq data This work GEO: GSE231929 Experimental models: Cell lines E14TG2a, mouse embryonic stem cells American Type Culture Collection (ATCC) Cat# CRL-1821; RRID: CVCL_9108 Oligonucleotides Mx-TOP adapters for Ion Torrent sequencing: A1, 5’-P-GATTGGAAGAGTGGTTCAGCAGGA ATGCTGAG and A2, 5’-ACACTCTTTCCCTAC ATGACACTCTTCCAATCT Metabion N/A 2x-TOP TO (tethered oligonucleotide) for Ion Torrent sequencing: alkyne-TT-biotin-ODN, 50-TXTTTTGTGTGGTTTGGAGACTGACTACC AGATGTAACA-Biotin (X=C8-alkyne-dU) Base-click N/A 3x-TOP TO for Ion Torrent sequencing: amine-TT-biotin-ODN, 5‘-TXTTTTGTGTGGTT TGGA GACTGACTACCAGATGTAACA-Biotin (X = C2-amine-dT).
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