|
| Status |
Public on Jun 09, 2015 |
| Title |
MDA-MB-231_DGE |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: Basal-like 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_8
|
| 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 |
SRX154988 |
| BioSample |
SAMN01055216 |
