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metaSeq (version 1.12.0)

BreastCancer: Multiple RNA-Seq count data designed as Breast Cancer cell lines vs Normal cells

Description

A data frame with 23368 rows (genes) with following 18 columns (samples).

All reads were measured by Illumina Genome Analyzer II or IIX, trimmed as 36 base, and mapped to the human reference genome hg19 as single-end. Each experimental design was restricted as Breast cancer cell vs Normal cell. Quality Control was performed by FastQC and samples whose quality scores were at least over 20 were choosed. Counts are quantified by HTSeq.

Usage

data(BreastCancer)

Arguments

Details

StudyA: SRP008746
  • A_1: Breast Cancer (HCC1937), SRX099961, SRR350976

  • A_2: Breast Cancer (HCC3153), SRX101334, SRR353604_1

  • A_3: Breast Cancer (SUM131502), SRX101335, SRR353948_1

  • A_4: Normal (MCF10A), SRX099963, SRR353603_1

  • A_5: Normal (HCC2337), SRX101336, SRR353602_1

StudyB: SRP006726

  • B_1: Breast Cancer (HCC1954), SRX061997, SRR201983

  • B_2: Normal (HMEC), SRX061998, SRR201986

    • StudyC: SRP005601

    • C_1: Breast Cancer (BT20), SRX040501, SRR097786_1

  • C_2: Breast Cancer (BT474), SRX040502, SRR097787_1

  • C_3: Breast Cancer (MCF7), SRX040504, SRR097789_1

  • C_4: Breast Cancer (MDAMB231), SRX040505, SRR097790_1

  • C_5: Breast Cancer (MDAMB468), SRX040506, SRR097791_1

  • C_6: Breast Cancer (T47D), SRX040507, SRR097792_1

  • C_7: Breast Cancer (ZR751), SRX040508, SRR097793_1

  • C_8: Normal (MCF10A), SRX040503, SRR097788_1

    • StudyD: ERP000992

    • D_1: Breast Cancer (MCF7), ERX030989, ERR053953

  • D_2: Breast Cancer (T47D), ERX031000, ERR053958

  • D_3: Normal (Ishikawa), ERX030994, ERR053948

    • References

    Hon, G. C. and Hawkins, R. D. and Caballero, O. L. and Lo, C et al. (2012) Global DNA hypomethylation coupled to repressive chromatin domain foormation and gene silencing in breast cancer. Genome Research, 22 (2): 246-258

    Sun, Z. and Asmann, Y. W. and Kalari, K. R. and Bot, B. et al. (2011) Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLOS ONE, 25;6(2): e17490

    See Also

    StudyA, pvals.

    Examples

    Run this code
    data(BreastCancer)

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