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Sample GSM1693047 Query DataSets for GSM1693047
Status Public on Jun 09, 2015
Title 21NT_RNAseq
Sample type SRA
 
Source name Breast cancer cells
Organism Homo sapiens
Characteristics cell type: Luminal cells
cell line: 21NT
Extracted molecule total RNA
Extraction protocol polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec). PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification, the final library was purified with Ampure XP beads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Basecalls performed using CASAVA version 1.7 or 1.8.
RNA-Seq raw data was mapped by Tophat to hg19.
Genome_build: hg19
Supplementary_files_format_and_content: text file of normalized count data (FPKM). the file consists of following columns (tracking_id, class_code,nearest_ref_id, gene_id, gene_short_name, tss_id,locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status)
 
Submission date May 21, 2015
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 GPL18573
Series (2)
GSE38548 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer
GSE69114 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [RNA-Seq]
Relations
BioSample SAMN03703666
SRA SRX1035156

Supplementary file Size Download File type/resource
GSM1693047_21NT.genes.fpkm_tracking.gz 803.6 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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