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Sample GSM622199 Query DataSets for GSM622199
Status Public on Dec 10, 2010
Title breast_epithelium_cancer_SSEA4_IDC38
Sample type SRA
Source name biopsy and surgery
Organism Homo sapiens
Characteristics tissue: breast
cell type: epithelial cell
disease state: cancer
cell marker: SSEA4+
antibody vender: R&D Systems
antibody catalog #: MAB1435
Extracted molecule polyA 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.
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 Nov 11, 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)
GSE25291 Altered antisense-to-sense transcript ratios in breast cancer: Sage-Seq
GSE25292 Altered antisense-to-sense transcript ratios in breast cancer
SRA SRX033290
BioSample SAMN00149476

Supplementary file Size Download File type/resource
GSM622199_SSEA4_IDC38_tag.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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