Dataset features

Specifications


Application: RNA-seq analysis, sRNA-seq analysis
Number of samples: 99
Release date: Aug 24 2012
Last update date: Nov 14 2017
Access: Public
Diseases: Breast Neoplasms, Carcinoma, Squamous Cell, Neoplasms, Sarcoma, Brachydactyly
Chemicals: Estrogens
Dataset link Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel of archived human cancers

Experimental Protocol


3SEQ was performed on 64 formalin-fixed, paraffin-embedded (FFPE) human tumors representing 17 diagnostic cancer subtypes. Duplicate libraries were prepared for two of the tumors (ESS STT5520 and LMS STT516). 3SEQ was also performed on 27 normal human tissue samples. RNA-Seq was performed on 6 breast cancer cell lines for the examination of the breast-specific transcript on chr10. Series supplementary files: 'GSE28866_raw_counts_54511_peaks_cancer_and_normal.txt': Raw_counts: Total 3SEQ reads in each peak for each sample. File includes read counts for 54,511 peaks for the 66 cancer libraries and the 27 normal libraries. 'GSE28866_36048_normalized_peaks_cancer_and_normal.txt': Normalized_peaks: Normalized 3SEQ expression data for the 36,048 filtered peaks for the 66 cancer libraries and the 27 normal libraries. Peaks were classified as coding, lncRNA (Rinn, Bartel, Hughes, Gencode_lnc), other known transcripts (ref_known_Gencode_nc, all_mrna, other known), downstream, intron, promoter, or novel_intergenic. Peaks determined to be differentially expressed in one of the 17 cancer subtypes using a series of 2-Class SAM analyses are noted along with the type of cancer showing upregulation. Expression data was normalized using the sequencing depth of each sample by scaling the data using the mean value of each sample. Data was further compressed to reduce outliers by taking the square root of each value.

Repositories


GEO

GSE28866

ArrayExpress

E-GEOD-28866

ENA

SRP006575

BioProject

PRJNA140583

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Contact


Robert West
Robert B. West