Title

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

Document Type

Dataset

Publication Date

2015

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 A.1, and these documents were named according to the sample type (Sham, AdjDBC, TumDBC, AdjBaP and TumBaP) and replicate (A, B and C). Table A.2 provides a description of the file content according to the spreadsheet column title.

TABLE A.1[ADB1]

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

Sham_A_553635A01_ratio_peaks_mapToFeatures_All_Peaks.xls

Sham_B_553565A03_ratio_peaks_mapToFeatures_All_Peaks.xls

Sham_C_553574A01_ratio_peaks_mapToFeatures_All_Peaks.xls

AdjDBC_A_553634A03_ratio_peaks_mapToFeatures_All_Peaks.xls

AdjDBC_B_553654A03_ratio_peaks_mapToFeatures_All_Peaks.xls

AdjDBC_C_553635A02_ratio_peaks_mapToFeatures_All_Peaks.xls

TumDBC_A_553634A01_ratio_peaks_mapToFeatures_All_Peaks.xls

TumDBC_B_553565A01_ratio_peaks_mapToFeatures_All_Peaks.xls

TumDBC_C_553653A03_ratio_peaks_mapToFeatures_All_Peaks.xls

AdjBaP_A_553653A02_ratio_peaks_mapToFeatures_All_Peaks.xls

AdjBaP_B_553653A01_ratio_peaks_mapToFeatures_All_Peaks.xls

AdjBaP_C_553565A02_ratio_peaks_mapToFeatures_All_Peaks.xls

TumBaP_A_553635A03_ratio_peaks_mapToFeatures_All_Peaks.xls

TumBaP_B_553574A03_ratio_peaks_mapToFeatures_All_Peaks.xls

TumBaP_C_554845A01_ratio_peaks_mapToFeatures_All_Peaks.xls

TABLE A.2

Definitions of File Contents for Appendix A 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

[ADB1]If this content doesn’t work, then I can amend the text above to refer back to the thesis itself.

readmeA.docx (129 kB)
MD5: 58b35779ed5fe1cc532b2e6feb2241f6

Fish MS Thesis Appendix A. NimbleGen Processed Data Report for All Methylated Peaks.zip (6776 kB)
MD5: 483e055fbcb4f52062f882d17ec217e2

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