|
| Status |
Public on Oct 05, 2010 |
| Title |
epitheliumbreast-cancer-C6 |
| Sample type |
SRA |
| |
|
| Source name |
biopsy and surgery
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
cell type: epithelial cell
disease state: cancer
cell marker: EPCR
|
| Extracted molecule |
total 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.
Details of antibodies used in study:
CD24-Antibody: Vendor: BD-Pharmingen, Cat.#: 555426
CD44-Antibody: Vendor: BD-Pharmingen, Cat.#: 550988
CD201(EPCR)-Antibody: Vendor: BD-Pharmingen, Cat.#: 552500
|
| |
|
| 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 |
Oct 01, 2010 |
| 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 |
GPL9052 |
| Series (3) |
| GSE24491 |
Gene expression profiling of human tissue samples using SAGE-Seq |
| GSE25291 |
Altered antisense-to-sense transcript ratios in breast cancer: Sage-Seq |
| GSE25292 |
Altered antisense-to-sense transcript ratios in breast cancer |
|
| Relations |
| SRA |
SRX027820 |
| BioSample |
SAMN00115003 |
