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Sample GSM636919 Query DataSets for GSM636919
Status Public on Dec 10, 2010
Title ASSAGE_breast_epithelium_cancer_T1
Sample type SRA
Source name biopsy and surgery
Organism Homo sapiens
Characteristics tissue: breast
cell type: epithelial cell
disease state: cancer
cell marker: CD24+
Extracted molecule polyA RNA
Extraction protocol ASSAGE libraries were generated essentially as described (PMID: 19056939), except that we used polyA RNA. Briefly,we treated polyA RNA with bisulfite, which changes all cytidine residues to uridine residues. We generated cDNA from bisulfite-treated RNA with reverse transcriptase, the double-stranded cDNA was used to construct libraries for sequencing following Illumina's standard genomic DNA sample preparation instructions. The sequence of a bisulfite-treated RNA molecule can only be matched to one of the two possible DNA template strands.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
Data processing We generated a bisulfite-converted genome for both plus and minus strands (6.2 Gb) as a reference for ASSAGE reads. We used SeqMap ( align reads to the bisulfite-converted genome under default conditions, allowing up to two mismatches in 32-bp reads. We used reads that uniquely mapped to either plus or minus strand-derived sequences.
Submission date Dec 08, 2010
Last update date May 15, 2019
Contact name Kornelia Polyak
Phone 617-632-2106
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Polyak
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platform ID GPL9052
Series (2)
GSE25292 Altered antisense-to-sense transcript ratios in breast cancer
GSE25932 Altered antisense-to-sense transcript ratios in breast cancer: ASSAGE
SRA SRX033236
BioSample SAMN00149456

Supplementary file Size Download File type/resource
GSM636919_ASSAGE_T1_tagAlign.bed.gz 46.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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