Readme - AKSchmid Duke Digital Repository 

Data are reported in Dulmage et al., submitted. “Copy number variation is associated with gene expression change in archaea”.

See also github repository associated with this paper - https://github.com/amyschmid/Halobacterium_CNV

Files and folders
1. expression - Folder that contains gene expression microarray raw data, normalized data, metadata, and Python scripts by which raw data were normalized.

a. S8_Table_rev_metadata.xlsx. Contains normalized data on one tab and metadata corresponding to each column header for each experiment on the other tab. Table S8 is supplementary table 8 in the publication listed above.

b. expression_raw. Folder containing raw data as tab delimited text files. File names are unique identifiers corresponding to each experiment in the metadata tab of Table S8.

c. quantile_normalization.py. Python code for normalization. Raw data input are found in the “expression_raw” folder, normalized data output are in Table S8. This normalization strategy is different than those previously reported for this dataset (i.e. in Brooks et al., 2014, Molecular Systems Biology 10:740.)

2. ChIP - Folder that contains ChIP control gDNA microarray raw data, normalized data, metadata.

a. ChIP_raw. Folder containing raw data as text files. File names are correspond to each experiment in ChIP_metadata.xlsx.

b.  chip.all.med.txt -  File containing median normalized data (see Methods section for procedure). Names of arrays in the “ID” column correspond to raw data file names as detailed in “ChIP_metadata.xlsx”.

c. ChIP_metadata.xlsx - Metadata for ChIP experiments. Corresponds to paper Supplementary Table S1 “ChIP_analyzed” tab. Lists ID (unique ID used throughout analysis), raw data file name, and other metadata for each array.

d. ChIP_array_processing2.R - Custom R scripts used for processing and normalizing ChIP data.