wormencode

ChIP-chip_normalization_standard_zscore_v1.doc (median centered)

ChIP-chip_normalization_standard_zscore_v2.doc (mean centered)

ChIP-chip_normalization_standard_MA2C_v1.doc

ChIP-chip_normalization_standard_nimblegen_v1.doc

Peak finding protocols

ChIP-chip_peak_finding_Chipotle

ChIP-chip_peak_finding_MA2C

Since these protocols will be specific for each dataset, please create your protocols with your initial+version# and put it in the Custom Protocols below.

Worm DAPI staining

Worm_DAPI_staining_v3

Protocol Change Policy

Before any official protocol is altered, evidence that the alteration is an improvement must be posted to the wiki, and the suggested change should be discussed on a conference call and approved by the group. Exceptions include typos or changes to the format or organization of the protocol, but even these should be designated as new versions. See Naming Conventions for naming protocols.

Custom Worm Chromatin Group Protocols

Initials: CW, Christina Whittle; PK, Paulina Kolasinska-Zwierz; RG, Reto Gassmann; TP,Taryn Phippen; SE, Sevinc Ercan; SS, Susan Strome; KI, Kohta Ikegami; HP, Hoang Pham; AD, Andrea Dose

Worm embryo growth and harvest

Worm_embryo_growth_and_harvest_vCW1.doc

Worm_embryo_growth_and_harvest_vRG1.doc

Worm_embryo_growth_and_harvest_vSS1.doc

Worm_embryo_growth_and_harvest_vSE1.doc

Worm_embryo_growth_and_harvest_vSS6.doc

Worm_embryo_growth_and_harvest_vSS5.doc

Worm_embryo_growth_and_harvest_vSS4.doc

Worm_embryo_growth_and_harvest_vSS3.doc

Worm_embryo_growth_and_harvest_vSS2.doc

Worm embryo extraction

Worm_embryo_extraction_vCW1.doc

Worm_embryo_extraction_vRG1.doc

Worm_embryo_extraction_vSS1.doc

Worm_embryo_extraction_vSE1.doc

Worm_embryo_nuclei_preparation_vKI1.doc

Worm_embryo_extraction_vSS5.doc

Worm_embryo_extraction_vSS4.doc

Worm_embryo_extraction_vSS3.doc

Worm_embryo_extraction_vSS2.doc

Worm L3 growth and harvest

Worm_L3_growth_and_harvest_vPK1.doc

Worm L3 extract

Worm_L3_extraction_vPK1.doc

Worm L4 growth and harvest

Worm_L4_growth_and_harvest_vSE1.doc

Worm Adult growth and harvest

Worm_Adult_growth_and_harvest_vHP1.doc

Worm Adult extract

Worm_adult_extraction_vHP1.doc

Worm chromatin immunoprecipitation

Worm_chromatin_immunoprecipitation_vCW1.doc

Worm_chromatin_immunoprecipitation_vPK1.doc

Worm_chromatin_immunoprecipitation_vRG1.doc

Worm_chromatin_immunoprecipitation_vSS1.doc

Worm_chromatin_immunoprecipitation_vSS2.doc

Worm_chromatin_immunoprecipitation_vSS3.doc

Worm_chromatin_immunoprecipitation_vHP1.doc

Worm_chromatin_immunoprecipitation_vKI1.doc

Worm_chromatin_immunoprecipitation_vKI2.doc

Worm_chromatin_immunoprecipitation_vKI3.doc

PAIRE

Worm_SonicPAIRE_vKI1.doc

Worm_SonicPAIRE_vKI2.doc

Worm_MNasePAIRE_vKI1.doc

Worm LM-PCR Amplification for ChIP-chip

Worm_LM-PCR_Amplification_for_ChIP-chip_vPK1.doc

Worm_LM-PCR_Amplification_for_ChIP-chip_vRG1.doc

Worm_LM-PCR_Amplification_for_ChIP-chip_vSS1.doc

Worm_LM_PCR_Amplification_from_MNaseDNA_vKI1.doc

Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2.doc

Worm_LM-PCR_Amplification_for_ChIP-chip_vKI1.doc

Worm_LM-PCR_Amplification_for_ChIP-chip_vKI2.doc

Normalization Protocols

ChIP-chip_normalization_custom_zscore_vSE1.doc

Peak finding protocols

ChIP-chip_peak_finding_ChIPOTle_vCW1.doc

ChIP-chip_peak_finding_ChIPOTle_vSE1.doc

Peak finding protocols

(ChIP-chip_peak_finding_Chipotle)

(ChIP-chip_peak_finding_MA2C)

Protocol name track

You can see how protocol names have been changed in the table below.

Open the table in this browser

Protocol Development Track

Protocols under development that may become official pending further testing.

Extract prep and ChIP Ahringer lab extract prep and ChIP protocol

Extract prep and ChIP protocol used by Paulina for the L3 ChIP on chip Ahringer lab extract prep and ChIP protocol used by Paulina for L3 ChIP on chip experiment

Worm Nuclear Prep Abby's nuclear isolation (whole worm)

Liquid culture growth and harvest Ahringer lab liquid culture

qPCR from ChIP Ahringer lab qPCR protocol (also have previous version ChIP-QPCR Protocol (Ahringer Lab))

WormGrowth_Taryn_10_08_07.doc Taryn's worm growth protocol

Extract&ChIP_Taryn_4_18_07.doc Taryn's extract & ChIP protocol

premodENCODE_ChIP_protocol_Desai.doc Pre-modENCODE protocol used for CENP-A ChIP (Desai Lab)

Supplementary Protocols

Protocols for procedures that are not officially part of the modENCODE grant but useful to the group.

Western Blot-CW121905.doc

Western_SE_052007.doc

Detailed protocol for liquid N2 culture.doc A section (in red) is added to the 'Embryo Growth and Harvest Protocol (v5)' containing details on setup and maintenance of the liquid culture.

L3_N2_20C_collection_protocol.doc

subbing slides Treatment of glass slides for immunostaining or FISH procedures

Amplification_Taryn_8_30_07.doc Taryn's LM-PCR amplification protocol

Gateway Manual (Ahringer Lab)

Gateway Primer (Ahringer Lab)

Gateway Primer Table (Ahringer Lab)

Definitive Table Primer Gateway (Ahringer Lab)

P UNC HB101.rtf HB101 growth protocol from University of Alabama Fermentation Facility (Sevinc)(Lieb Lab)