BreastCancer {metaSeq} | R Documentation |
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.
data(BreastCancer)
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
https://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP008746
http://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP006726
http://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP005601
http://trace.ddbj.nig.ac.jp/DRASearch/study?acc=ERP000992
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
data(BreastCancer)