Incubation:Article Title: Identification of Parkinson’s disease-associated regulatory variants in human dopaminergic neurons reveals modulators of SCARB2 and BAG3 expression
Article Snippet: DNA digestion was performed by adding 20 μl of 10X NEB2.1 buffer with 15 μl of MboI restriction enzyme (NEB R0147L, New England Biolabs) and incubated at 37°C for 45 minutes in a thermomixer at 450 rpm. .. After 45 minutes, 5 μl of MboI restriction enzyme (NEB R0147L, New England Biolabs) was added again and incubated at 37°C for 45 minutes in a thermomixer at 450 rpm to increase digestion efficiency. ..
Article Title: Identification of Parkinson’s disease-associated regulatory variants in human dopaminergic neurons reveals modulators of SCARB2 and BAG3 expression
Article Snippet: SDS was quenched by adding 12.5 μl of 10% Triton X-100 (Sigma-Aldrich, X100) and 50 μl of nuclease-free water and incubated at 37°C for 45 minutes in a thermomixer at 650 rpm. .. DNA digestion was performed by adding 20 μl of 10X NEB2.1 buffer with 15 μl of MboI restriction enzyme (NEB R0147L, New England Biolabs) and incubated at 37°C for 45 minutes in a thermomixer at 450 rpm. .. After 45 minutes, 5 μl of MboI restriction enzyme (NEB R0147L, New England Biolabs) was added again and incubated at 37°C for 45 minutes in a thermomixer at 450 rpm to increase digestion efficiency.
Article Title: Multi-omic gene regulatory networks informed by 3D chromatin architecture reveal insights into hematopoietic stem cell ageing
Article Snippet: Cells were then lysed in lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% Igepal CA630) with 50μl of protease inhibitors (Sigma, #P8340), washed with lysis buffer without protease inhibitors, then nuclei were placed in 0.5% sodium dodecyl sulfate (SDS) and incubated at 62°C for 10 minutes. .. The SDS was then quenched with 10% Triton X-100 (Sigma, #93443) for 15 mins at 37°C, then 100U of MboI restriction enzyme (NEB, #R0147) was added and the mixture incubated at 37°C overnight. .. The MboI enzyme was inactivated by heating to 62°C for 20 minutes, DNA fragment ends were biotinylated by incubating nuclei with biotin-14-ATP, dCTP, dGTP and dTTP and 5□U/μL DNA polymerase I Klenow (NEB, #M0210), then incubating at 37°C for 90 minutes with rotation.
Hi-C:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Lysis:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Labeling:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Ligation:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
DNA Purification:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Isolation:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Purification:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Sonication:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Adapter Ligation:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Polymerase Chain Reaction:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Amplification:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Sequencing:Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [ ]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
Article Title: TCF3 activates super-enhancer-driven TRIB2 overexpression to suppress ferroptosis and promote hepatoblastoma proliferation.
Article Snippet: .. Hi-C libraries were prepared according to previously described methods [27]. (1) Crosslinking: Samples were treated at room temperature with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. (2) Lysis: Fixed cells were subsequently disrupted using lysis buffer. (3) Chromatin processing: Endogenous nucleases were inactivated with 0.3% SDS, and chromatin was digested using the MboI restriction enzyme (100 units, New England Biolabs, NEB, Ipswich, MA, USA). (4) Labeling and ligation: DNA ends were labeled with biotin-14-dCTP (Invitrogen, Carlsbad, CA, USA) and ligated with T4 DNA ligase (50 units, NEB). (5) DNA purification: After reversing the crosslinks, ligation products were isolated using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). (6) Library preparation: Purified DNA was fragmented by sonication (300–500 bp), subjected to blunt-end repair, A-tailing, and adapter ligation, followed by streptavidin-mediated enrichment of biotinylated fragments and PCR amplification. (7) Sequencing: The final libraries were quality-controlled and sequenced on MGI-Seq platforms (BGI, China). ..
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New England Biolabs is a verified supplier 
New England Biolabs manufactures this product 