Subject: Co-localization and cluster analyses data for paper "Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress"
Date: 10-09-2020
Contacts: Beverly M. Emerson (emersobe@ohsu.edu), Bettina J. Lehman (bienchenbareiss@aol.com)
Affliation: Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America

This directory contains all data for the co-localization and cluster analyses included in the following paper
"Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress"

Files for different figures were organized in separate folders. See below for more details.

PART I: Co-localization analysis
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Fig_4A_colocalization_analysis:

- Coloc_CTCF-H3_and_CTCF-DAPI: Files used for Co-localization of CTCF-H3 and CTCF-DAPI. 
    - ims_files: Analyzed Imaris files
    - czi_files: Raw czi files.

- Coloc_CTCF-SC-35: Files used for Co-localization of CTCF-SC-35.
    - ims_files: Raw Imaris files
    - czi_files: Raw czi files.
    - creation_parameters: Imaris creation parameter .icpx files for batch processing 

PART II: Cluster analysis
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Fig_4C_CTCF_cluster_analysis:

- czi_files: raw czi files of Sample 1-5
- ims_files
    - raw_ims: raw Imaris files of Sample 1-5
    - preprocessed_ims: Background subtracted (twice) Imaris files of Sample 1-5
- creation_parameters: Creation parameters used for Imaris batch processing
- stats: Summary of statistics of CTCF and SC-35

Images were encripted and analyzed blindly. Unencrypted information can be found below:
Sample 1. HMEC + H2O2. 
(staining: green: SC-35, red: CTCF). This is the treated sample.
Sample 2. HMEC negative control. 
(staining: green: SC-35, red: NONO, which is a nuclear speckle not co-localizing with SC-35, but can by itself show small cluster formation)
Sample 3. HMEC positive control. 
(staining: green: hnRNP-K, which is another protein that should form clusters at SC-35, red: CTCF, should look similar to Sample 4)
Sample 4. HMEC untreated. 
(staining: green: SC-35, red: CTCF)
Sample 5. vHMEC. 
This is a pre-cancer version of normal HMEC(staining: green: SC-35, red: CTCF)

Note: Sample 3 were used as as a positive control for cluster and sample 2 was used as a negative control to figure out how to best identify and meassure a cluster. 


Fig_6C_CTCF_cluster_analysis:

- czi_files: raw czi files of condition NPC and NPC-H2O2 
- ims_files
    - raw_ims: raw Imaris files of condition NPC and NPC-H2O2 
    - preprocessed_ims: Background subtracted (twice) Imaris files of condition NPC and NPC H2O2
- creation_parameters: Creation parameters used for Imaris batch processing
- stats: Summary of statistics