Brandon Sos: Difference between revisions
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==Current Projects== | ==Current Projects== | ||
* [[Brandon:LAB/DNA_accessibility|DNA accessibility w/ Nextera kit project]] | * [[Brandon:LAB/DNA_accessibility|DNA accessibility w/ Nextera kit project]] | ||
==Protocols== | ==Protocols== | ||
[[Brandon:Protocols/DNA_gel | DNA gel]] | [[Brandon:Protocols/DNA_gel | polyacrylamide DNA gel]] | ||
[[Brandon:Protocols/TBU_gel | TBU gel]] | |||
[[Brandon:Protocols/Count_Cells | Count cells]] | [[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 | *notes | ||
**minielute colums for <10 ul samples, otherwise use qiaquick columns | **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== | ==Main Calendar== | ||
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<calendar> | <calendar> | ||
name=Brandon:LabNotes/Project1 | name=Brandon:LabNotes/Project1 |
Latest revision as of 23:41, 1 February 2017
Current Projects[edit]
Protocols[edit]
AMPure XP beads purification only (for >= 5 ng)
AMPure XP beads purification 2-step PCR (for <=5 ng)
Invitrogen MAXIscript T7 In vitro transcription kit
SMART MMLV RT protocol (for first strand synthesis)
standard PCR cycling for for different enzymes etc
enzyme reaction buffer compositions
tn5 production protocol updated R3 (7/30/2014)
tn5 production protocol updated R4 (9/3/2014)
Nextera V1 protocol sequences detail
original T7-top protocol sequences detail
Nextera_XT_V2_sequences_and_outline_sequences_detail
THS-seq protocol updated to using Nextera XT V2 sequences detail
- notes
- minielute colums for <10 ul samples, otherwise use qiaquick columns
- N2 adaptor is illuminia adaptor. Nextera adaptor is nextera adaptor
Main Calendar[edit]
<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>