Category Archives: Protocols

Revised Fast OligoPaint Synthesis

Posted on October 9, 2013 by admin

Jeffrey Moffitt, Alistair Boettiger, Xiaowei Zhuang jeffmoffitt@gmail.com alistairboettiger@gmail.com Version 2.0: October 2013 Purpose and Overview This protocol describes the construction of OligoPaints FISH probes from a complex oligo library via reverse transcription of an RNA intermediate. By exploiting the high … Continue reading →

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Protected: New OligoPaints Protocol

Posted on August 26, 2013 by admin

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Demo Gist-based version management

Posted on March 1, 2013 by admin

Protocol: Oligo Paint Synthesis permalink to most recent version. permalink to the version as it stood when this demo was published on 03/21/13. Gist embedded version of date-specific permalink using native Gist embed interpreter for markdown: [easyembed field=”Gist1″]

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demo: version managed pdf protocol

Posted on March 1, 2013 by admin

Protocol Qiagen Miniprep (QIAprep) Latest Updated version. Date specific version

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Large Scale PCR for probe synthesis

Posted on February 28, 2013 by admin

Part 1 – PCR amplification Notes: We recommend setting up 10 ml of PCR master mix and aliquoting it into a 96-well plate, 100 µl per well. This protocol is scaled for a starting amount of 10 ml; simply scale … Continue reading →

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Emulsion PCR

Posted on February 28, 2013 by admin

For initial amplification from Oligo-Library. Setup Components Glass vials kept at -20C. magnetic stir plates at 4C/in cold room (capable of 1000 rpm) emulsion oil mix (can make in 50mL volume and store at 4C): 80 uL ABIL EM90 (request … Continue reading →

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STORM Buffers

Posted on February 23, 2013 by admin

TCEP Buffer 0.2M Tris pH 9  (200 uL Tris 1M pH 9.0) 1 mM Methyl viologen (10 uL of 0.1 M stock.  Currently make fresh from powder. Toxic) (25.7 mg / mL) 1 mM Ascorbic Acid (10 uL of 0.1 … Continue reading →

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Subbing Coverglass for STORM tissue-sections

Posted on February 5, 2013 by admin

Materials Thomas CoorsTek ceramic coverglass holders (2) 1M KOH (56.11 g KOH in 1000 ml H2O) 600 ml pyrex beakers (2) Gelatin (from bovine skin type B) Chromium potassium sulfate 95% EtOH (ethanol) Methods Place coverglass in ceramic holders: for … Continue reading →

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DNA FISH on coverglass

Posted on January 23, 2013 by admin

Adopted from Wu lab protocol.  01/23/13 Briefly wash cells with 1x PBS (not PBT) Fix cells with 4% formaldehyde for 15 min Quick wash with 1x PBS Wash cells with 2x SSCT for 5 min Wash cells with 50% formamide/2x … Continue reading →

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Denaturing PAGE

Posted on January 20, 2013 by admin

(Adapted from Bryan Harada’s protocol, 02/25/12). for Extraction of single stranded DNA probes Materials: 2x Loading Buffer (96% formamide/20mM EDTA, prepare using freshly deionized formamide) Acrylamide/Bis 19:1 40% (w/v) Solution   TEMED 10% APS (w/v). make fresh from powder and … Continue reading →

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