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==Current Projects== * [[Brandon:LAB/DNA_accessibility|DNA accessibility w/ Nextera kit project]] ==Protocols== [[Brandon:Protocols/DNA_gel | polyacrylamide DNA gel]] [[Brandon:Protocols/TBU_gel | TBU gel]] [[Brandon:Protocols/Count_Cells | Count cells]] [[Brandon:Protocols/primers_prep | Primers prep]] [[Brandon:Protocols/Lysis_buffers | Lysis buffers]] [[Brandon:Protocols/gel_size_selection | gel size selection]] [[Brandon:Protocols/AMPure_beads_purification | AMPure XP beads purification only (for >= 5 ng)]] [[Brandon:Protocols/AMPure_beads_purification2 | AMPure XP beads purification 2-step PCR (for <=5 ng)]] [[Brandon:Protocols/Cloning_Transformation3 | Cloning and Transformation.]] [[Brandon:Protocols/MAXIscript_T7_IVT | Invitrogen MAXIscript T7 In vitro transcription kit]] [[Brandon:Protocols/SMART_MMLV_RT | SMART MMLV RT protocol (for first strand synthesis)]] [[Brandon:Protocols/taq_amplification2 | standard PCR cycling for for different enzymes etc]] [[Brandon:Protocols/enzyme_rxn_buffers | enzyme reaction buffer compositions]] [[Brandon:Protocols/egel_protocol | e gel protocol]] [[Brandon:Protocols/qubit_protocol | qubit protocol]] [[Brandon:Protocols/agarose_gel_protocol | agarose gel protocol]] [[Brandon:Protocols/tn5_production | tn5 production protocol]] [[Brandon:Protocols/tn5_production_updated_7_30_2014 | tn5 production protocol updated R3 (7/30/2014)]] [[Brandon:Protocols/tn5_production_updated_9_3_2014 | tn5 production protocol updated R4 (9/3/2014)]] [[Brandon:Protocols/transposon_annealing | transposon_annealing]] [http://genome-tech.ucsd.edu/LabNotes/index.php/Brandon:LabNotes/Project1/2012-5-8 Nextera V1 protocol sequences detail] [http://genome-tech.ucsd.edu/LabNotes/index.php/Brandon:LabNotes/Project1/2012-5-7 original T7-top protocol sequences detail] [http://genome-tech.ucsd.edu/LabNotes/index.php/Brandon:LabNotes/Project1/2013-7-10 THS-seq_RNA_processing_with_double_stranded_cDNA_and_tn5_fragmentation_adaptor_addition_and_sequences_detail] [[Brandon:Protocols/Nextera_XT_V2_sequences_and_outline | Nextera_XT_V2_sequences_and_outline_sequences_detail]] [http://genome-tech.ucsd.edu/LabNotes/index.php/Brandon:LabNotes/Project1/2015-8-3 THS-seq protocol updated to using Nextera XT V2 sequences detail] [http://genome-tech.ucsd.edu/LabNotes/index.php/Brandon:LabNotes/Project1/2015-9-18 combinatorial barcoding using contiguity preserved barcoded Tn5 method with Nextera XT V2 sequences detail] [http://genome-tech.ucsd.edu/LabNotes/index.php/Brandon:LabNotes/Project1/2015-9-21 multiplex combinatorial cellular indexing adaptation to THS-seq using nXTv2 sequence detail and protocol] *notes **minielute colums for <10 ul samples, otherwise use qiaquick columns **N2 adaptor is illuminia adaptor. Nextera adaptor is nextera adaptor [[Brandon:Protocols/Scratch | Scratch for notes etc]] ==Main Calendar== <calendar> name=Brandon:LabNotes/Project1 format=%name/%year-%month-%day date=2017/02/01 view=twoyear </calendar> <calendar> name=Brandon:LabNotes/Project1 format=%name/%year-%month-%day date=2016/02/01 view=twoyear </calendar> <calendar> name=Brandon:LabNotes/Project1 format=%name/%year-%month-%day date=2015/02/01 view=twoyear </calendar> <calendar> name=Brandon:LabNotes/Project1 format=%name/%year-%month-%day date=2014/02/01 view=twoyear </calendar> <calendar> name=Brandon:LabNotes/Project1 format=%name/%year-%month-%day date=2013/02/01 view=twoyear </calendar> <calendar> name=Brandon:LabNotes/Project1 format=%name/%year-%month-%day date=2012/02/01 view=twoyear </calendar> <calendar> name=Brandon:LabNotes/Project1 format=%name/%year-%month-%day date=2011/02/01 view=twoyear </calendar>
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