Index by title

ENCODE ChIP-seq data Treatment Description

Treatment Description Label
None No special treatment or protocol applies No treatment or prot
4OHTAM_1uM_36hr (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) 4-OHTAM 1uM 36hr
DMSO_0.02pct_24hr 24 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) DMSO_0.02pct_24hr
EtOH_0.02pct 1 h with 0.02% Ethanol (Myers) EtOH 0.02% 1h
BPA_100nM_4hr 4 h with 100 nM Bisphenol A (Myers) BPA_100nM_4hr
DEX_100nM 1 h with 100 nM Dexamethasone (Myers) DEX_100nM
DEX_100pM 1 h with 100 pM Dexamethasone (Myers) DEX_100pM
DEX_1nM 1 h with 1 nM Dexamethasone (Myers) DEX_1nM
DEX_500pM 1 h with 500 pM Dexamethasone (Myers) DEX_500pM
DEX_5nM 1 h with 5 nM Dexamethasone (Myers) DEX_5nM
DMSO_4hr 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) DMSO_4hr
Estradiol_10nM_4hr 4 h with 10 nM Estradiol (Myers) Estradiol_10nM_4hr
EtOH_0.02pct 1 h with 0.02% Ethanol (Myers) EtOH 0.02% 1h
Genistein_100nM_4hr 4 h with 100 nM Genistein (Myers) Genistein_100nM_4

ENCODE ChIP-seq data Protocol Description

Protocol Description Label
PCR1x one 15-cycle round of PCR (Myers) PCR 1-round
PCR2x a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) PCR 2-round
v041610.1 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) biorupter, PCR 1-round
v041610.2 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) sonicator, PCR 1-round
v042211.1 Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) ChIP AMpure XP

March 2013 Questionnaire

Hello Workshop attendees. We were hoping that you could fill out a brief survey about your workshop experience.

March 2013 Epigenome Informatics Workshop Evaluation Form

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Log In Instructions

Log In Instructions for NEW Genboree Users (if you have previously created a Genboree account, your user name and password will not change)

Canned Output Data From Use Cases

All data from these use cases has been run in the following:

Introduction

Aleks' Talks

Alan's Talk - 450K

Karin Michels Talk (October 2012 Workshop)

Kim Siegmund Talk (October 2012 Workshop)

Use cases

Use Case #1 - Genomewide Patterns of Methylation Distinguishes Blood, Cerebellum, and Cortex

Use Case #2 - Clustering of Breast Cell Types (via Epigenome Atlas)

Use Case #5 - Methylation of Specific Regions Discriminate Tissues Types Better Than Others

Use Case #9 - Coordinated Changes of Epigenomic Marks Across Tissue Types

Use Case #13 - Analysis of Epigenomic Variation in Breast Tumors

Use Case #14 - ChIP-Seq and mRNA-Seq Data Analysis via the Genboree Workench

Use Case #15 - Spark tool for epigenomic data exploration

Use Case #16 - Differential Expression Analysis of Two Breast Cancer Cell Lines Using Cuffdiff

Other Useful Information

FAQs relating to the Epigenomics Toolset