|
| Status |
Public on Jul 22, 2018 |
| Title |
BT474_20_sorted_cells |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT474
diagnosis: breast cancer
|
| Growth protocol |
Breast cancer cell lines were cultured as per ATCC standard protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Immunomagnetic Enrichment and Fluorescence Activated Cell Sorting (IE/FACS) cells were spiked into phosphate buffered saline (PBS) and peripheral blood (PB) from healthy female donors.
RNA extracted from cells was polyA+ labelled and used to generate Helicos DGE or Illumina libraries following the manufacturer’s protocols. The modified cDNA molecules were subjected to sequencing by the Helicos Heliscope or Illumina Hiseq 2000 system
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Helicos HeliScope |
| |
|
| Description |
P14.2012-07-13T16_14_50.0232421511010.fc1.ch7_18
|
| Data processing |
Illumina Casava1.7 software (illumina) or IndexDPGenomic (Helicos) used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using BWA (Helicos) or TopHat (Illlumina).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. Differential expression was calculated at a significance of p<0.05 after Benjamini and Hochberg correction using a null model.
Genome_build: hg18
Supplementary_files_format_and_content: Table with RPKM values for each Sample.
|
| |
|
| Submission date |
Jul 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Vasu Punj |
| E-mail(s) |
vasupunj@gmail.com
|
| Organization name |
USC
|
| Street address |
Biggy Street
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL14761 |
| Series (1) |
| GSE71192 |
EpCAM Based Capture Detects and Recovers Circulating Tumor Cells From Subtypes of Breast Cancer Except Claudin-low |
|
| Relations |
| BioSample |
SAMN03892841 |
| SRA |
SRX1115284 |
