Title

DNA methylation in lung tissues of mouse offspring exposed in utero to polycyclic aromatic hydrocarbons: Appendix B. NimbleGen processed data report for nearest methylated peaks

Document Type

Dataset

DCMI Type

Dataset

File Format

.zip, .xls

Publication Date

2015

Embargo Period

2016

Language

eng

Comments

The .zip archive includes 15 individual digital Microsoft Excel documents, one for each sample hybridized to the NimbleGen mouse methylation array. Names of the individual Excel documents are provided in Table B.1, and these documents were named according to the sample type (Sham, AdjDBC, TumDBC, AdjBaP and TumBaP) and replicate (A, B and C). Table B.2 provides a description of the file content according to the spreadsheet column title.

TABLE B.1

List of File Names Included in the Archive File for Appendix B

  • Sham_A_553635A01_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • Sham_B_553565A03_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • Sham_C_553574A01_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • AdjDBC_A_553634A03_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • AdjDBC_B_553654A03_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • AdjDBC_C_553635A02_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • TumDBC_A_553634A01_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • TumDBC_B_553565A01_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • TumDBC_C_553653A03_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • AdjBaP_A_553653A02_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • AdjBaP_B_553653A01_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • AdjBaP_C_553565A02_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • TumBaP_A_553635A03_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • TumBaP_B_553574A03_ratio_peaks_mapToFeatures_Nearest_Peak.xls
  • TumBaP_C_554845A01_ratio_peaks_mapToFeatures_Nearest_Peak.xls

TABLE B.2

Definitions of File Contents for Appendix B by Spreadsheet Column Title.

  • Column - Description
  • PEAK_ID - An ID for each mapped peak
  • CHROMOSOME - Chromosome associated with peak
  • PEAK_START - First base of the peak on the chromosome
  • PEAK_END - Last base of the peak on the chromosome
  • PEAK_SCORE - Average −log10 p-value for probes in the peak region
  • FEATURE_TRACK - The annotation track against which peaks were mapped, which is the transcription start site for this data set
  • FEATURE_STRAND - Strand of the transcript
  • FEATURE_START - First base of the feature on the chromosome
    • Note: For the transcription start site, feature size is 1; therefore, start and end positions are the same.
  • FEATURE_END - Last base of the feature on the chromosome
  • FEATURE_TO_PEAK_DISTANCE - Distance from center of peak to the feature
  • Parent - Internal identification number of the transcript from which the transcript start site is generated
  • Accession - NCBI RefSeq Accession ID
  • Name - Gene symbol of the transcript
  • Description - Full gene name of the transcript
  • Ncbi_gene_id - NCBI Entrez GeneID of the transcript
  • Synonyms - Other alias symbol(s) of the transcript
  • attr1 (etc.) - Other available attributes for the transcript

Disciplines

Toxicology

License

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.

Identifier

http://dx.doi.org/10.15142/T3201B

Files

readmeB.txt (2 kB)
MD5: 3c59689e37fabc595c21bb84a01a0582

Fish MS Thesis Appendix B. NimbleGen Processed Data Report for Nearest Methylated Peaks.zip (6082 kB)
MD5: 537d698cfd2928fb3f99154bc789320d

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