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Sample GSM603087 Query DataSets for GSM603087
Status Public on Oct 05, 2010
Title epitheliumbreast-cancer-C4
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 total RNA
Extraction protocol cDNA made from polyA RNA isolated from purified cells using antibody attached to beads were fragmented with NlaIII/MmeI restriction enzyme with subsequent adapter ligation.
Details of antibodies used in study:
CD24-Antibody: Vendor: BD-Pharmingen, Cat.#: 555426
CD44-Antibody: Vendor: BD-Pharmingen, Cat.#: 550988
CD201(EPCR)-Antibody: Vendor: BD-Pharmingen, Cat.#: 552500
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
Description Sage-Seq
Data processing Sequencing was carried out at the Wistar Institute. The first 17bps of each read is used as a tag. The number of each unique tag is counted. Processed data file includes tag sequences (17bps) in the first column and counts (frequencies) in the second column. Illumina software pipeline OLB version 1.6, 1.7, 1.8 with CASAVA 1.5 was used for generation of sequence: frequency processed files.
Submission date Oct 01, 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 (3)
GSE24491 Gene expression profiling of human tissue samples using SAGE-Seq
GSE25291 Altered antisense-to-sense transcript ratios in breast cancer: Sage-Seq
GSE25292 Altered antisense-to-sense transcript ratios in breast cancer
SRA SRX027818
BioSample SAMN00115001

Supplementary file Size Download File type/resource
GSM603087_LSAGE_Breast_Carcinoma_CD24+_C4_IDC40.txt.gz 2.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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