This Mitocarta2.0_RAW_450Kdata readme.txt file was generated on 2022-02-23 by Susan Murphy



GENERAL INFORMATION

1. Title of Dataset: Sex-specific DNA methylation and associations with in utero tobacco smoke
exposure at nuclear-encoded mitochondrial genes

2. Author Information
	A. Principal Investigator Contact Information
		Name: Susan K. Murphy
		Institution: Duke University Medical Center
		Address: 701 W. Main Street, Duke PO Box 90534, Durham, NC 27701
		Email: susan.murphy@duke.edu

	B. Associate or Co-investigator Contact Information
		Name: Dillon E. King
		Institution: Duke University
		Address: 701 W. Main Street, Duke PO Box 90534, Durham, NC 27701
		Email: dillon.king@duke.edu

	

5. Information about funding sources that supported the collection of the data: 

Supported by the National Institute of
Environmental Health Sciences awards P01ES022831,
P42ES010356, P30ES011961, R01ES016772, R24ES028531
805 and T32ES021432; the National Institute of Diabetes and
Digestive and Kidney Disease award R01DK085173; the
United States Environmental Protection Agency award RD-
83543701-0; and the National Science Foundation award
GRFP DGE-1644868.


SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: None.

2. Links to publications that cite or use the data: In process (Epigenetics, in press)

3. Links to other publicly accessible locations of the data: None.

4. Links/relationships to ancillary data sets: Complete 450k dataset has not yet been published.

5. Was data derived from another source? yes/no. No
	A. If yes, list source(s): 

6. Recommended citation for this dataset: In process - Epigenetics (in press)


DATA & FILE OVERVIEW

1. File List: One file: Mitocarta2.0_RAW_450Kdata.csv, containing the raw Illumina HumanMethylation450 BeadChip DNA methylation values for Mitocarta2.0 genes for the individuals included in the published analysis.


2. Relationship between files, if important:  NA

3. Additional related data collected that was not included in the current data package: NA

4. Are there multiple versions of the dataset? yes/no  No
	A. If yes, name of file(s) that was updated: 
		i. Why was the file updated? 
		ii. When was the file updated? 


METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 

Originally described in:
DNA Methylation in Babies Born to Nonsmoking Mothers Exposed to Secondhand Smoke during Pregnancy: An Epigenome-Wide Association Study.
Fuemmeler BF, Dozmorov MG, Do EK, Zhang JJ, Grenier C, Huang Z, Maguire RL, Kollins SH, Hoyo C, Murphy SK.
Environ Health Perspect. 2021 May;129(5):57010. PMID: 34009014 

2. Methods for processing the data: 

Raw beta values for each of the relevant CpG probes that are annotated to any Mitocarta2.0 gene were extracted from the larger 450k dataset for analysis.

3. Instrument- or software-specific information needed to interpret the data: NA

4. Standards and calibration information, if appropriate: NA

5. Environmental/experimental conditions: 

Comparison of cord blood DNA methylation from babies exposed in utero to tobacco smoke versus controls whose mothers never smoked tobacco. 

6. Describe any quality-assurance procedures performed on the data: NA

7. People involved with sample collection, processing, analysis and/or submission:

Susan Murphy
Dillon King
Dillon Lloyd
Rachel Maguire
Cathrine Hoyo 


DATA-SPECIFIC INFORMATION FOR: [Mitocarta2.0_RAW_450Kdata.csv]

1. Number of variables: 3 

2. Number of cases/columns: 381

3. Variable List: 

Methylation beta values for cg probes annotated to Mitocarta2.0 genes, where 1=methylated and 0=unmethylated
Sex: 1=male, 2=female
Maternal Tobacco Smoke Exposure: 0=nonsmoker, 1=smoker



4. Missing data codes: "NA"

5. Specialized formats or other abbreviations used: NA