|
| Status |
Public on Sep 28, 2016 |
| Title |
Breast_Tumor_Fibroblast_1 |
| Sample type |
SRA |
| |
|
| Source name |
Fibroblast from breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue of origin: breast tumor
|
| Growth protocol |
Fibroblasts were expanded in 50/50 mixture of DMEM-F12, 10% FBS/MEGM with supplements.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was extracted using the uMACS mRNA Isolation (Columns) kit (130-075-201). RNA concentrations were measured and quality controlled on a Bioanalyzer
RNAseq libraries were generated by Center for Cancer Computational Biology (CCCB) at Dana-Farber Cancer Institute following manufacture protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-Seq: Basecalls were performed using CASAVA version 1.8.2
RNA-Seq: Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics)
RNA-Seq: The datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version 2.3.1) using the default parameters.
RNA-Seq: The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using the default parameters and the hg19 refGene annotation file available at the UCSC Genome Browser.
processed data files format and content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.
Genome_build: hg18
|
| |
|
| Submission date |
Apr 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Muhammad B Ekram |
| E-mail(s) |
muhammad_ekram@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Kornelia Polyak Lab
|
| Street address |
450 Brookline Avenue, DA 740A
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE80333 |
Spatial proximity to fibroblasts impacts molecular features and therapeutic sensitivity of breast cancer cells influencing clinical outcomes |
|
| Relations |
| BioSample |
SAMN04858684 |
| SRA |
SRX1707758 |
