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| Status |
Public on Jun 09, 2015 |
| Title |
SUM159MDA453_RNAseq |
| Sample type |
SRA |
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| Source name |
Breast cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Heterofusion
cell line: SUM159PT-MDA-MB-453
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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)
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| Submission date |
May 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
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| Phone |
617-632-2106
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| Organization name |
Dana-Farber Cancer Institute
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| Department |
Medical Oncology
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| Lab |
Polyak
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| Street address |
450 Brookline Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| 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] |
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| Relations |
| BioSample |
SAMN03703673 |
| SRA |
SRX1035163 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1693054_SUM159MDA453.genes.fpkm_tracking.gz |
810.9 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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