Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms

Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms

Cardozo-Gizzi, et al. 2018

Data
====

# Data are submitted in 5 files (pairwise_distances_FigX.mat), see below for description.
# These files each contain a single structure (rawData) with the data organized as follows:

rawData.distanceMatrix
rawData.barcodesGenomicPositions contains the identities of the barcodes used ordered by genomic position
rawData.listofBarcodesGenomicallySorted contains the genomic positions of each barcode used.

These files can be opened with MATLAB.
The first field (distanceMatrix) contains the list of pairwise distances and corresponding genomic distances measured.
The data can be accessed as follows:

#To retrieve the genomic distances between barcode1 and barcode2, type

> distanceMatrix(1,2).genomicDistance

These distances are in kb.

# To retrieve the genomic distances between barcode1 and barcode2, type

> distanceMatrix(1,2).distance

These distances are in pixel units. A pixel represents 105 nm.

Datasets:
---------
/Cardozo_data/pairwise_distances_Fig1.mat (nc14 data)
/Cardozo_data/pairwise_distances_Fig3_nc12-13.mat
/Cardozo_data/pairwise_distances_Fig3_mitosis.mat
/Cardozo_data/pairwise_distances_Fig4_RNAon.mat (nc14, cells expressing sna)
/Cardozo_data/pairwise_distances_Fig4_RNAoff.mat (nc14, cells not expressing sna)

Matlab Code
===========

M-files (matlab code) can be found in folder 'HiM_pipeline_analysis'

merfish_main.m is the main routine that analyses deconvolved images to produce structures with barcodes localizations in each cell. The program is separated in well-annotated blocks that have to be run in a sequential manner. All other subroutines (functions) are called from merfish_main or functions therein.