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Sample GSM949585 Query DataSets for GSM949585
Status Public on Jun 09, 2015
Title MCF7_DGE
Sample type SRA
 
Source name Breast cancer cells
Organism Homo sapiens
Characteristics cell line: MCF7
cell type: Luminal cells
Extracted molecule total RNA
Extraction protocol PolyA+ RNA was extracted from breast cancer cells using a micro-MACS RNA purification kit (Miltenyi Biotec). Helicos DGE libraries were constructed following the manufacturer’s protocols. Briefly, 250ng of polyA RNA was converted to first strand cDNA molecules, and digested. The cDNA molecules were modified with PolyA tails of a controlled length and modified with a dideoxy nucleotide. The modified cDNA molecules were subjected to sequencing by the Helicos Heliscope system.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Helicos HeliScope
 
Description DGE_4
Data processing Reads were aligned to UCSC gene tracks using IndexDPgenomic (hg18). Reads aligning to ribosomal and mitochondrial transcripts were discarded. Aligned reads were normalized to reads per million for comparison. No length correction was performed.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include normalized count for each gene. Aligned reads were normalized to reads per million for comparison. No length correction was performed.
 
Submission date Jun 18, 2012
Last update date May 15, 2019
Contact name Kornelia Polyak
E-mail(s) kornelia_polyak@dfci.harvard.edu
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 GPL14761
Series (2)
GSE38548 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer
GSE38790 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [DGE]
Relations
SRA SRX154984
BioSample SAMN01055212

Supplementary file Size Download File type/resource
GSM949585_MCF7_RPM.txt.gz 120.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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