|
| Status |
Public on Sep 28, 2016 |
| Title |
Cancer_associated_fibroblasts |
| Sample type |
SRA |
| |
|
| Source name |
Fibroblast from breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue of origin: breast tumor
|
| Growth protocol |
All the epithelial and fibroblast cell lines were grown in media representing 50/50 mixture of DMEM-F12, 10% FBS/MEGM with supplements, as this media fully supported growth and viability of both epithelial cells and fibroblasts. Matrigel 3d culture experiments were performed using on-top method as described in Lee et al., Nature Methods, 2007 (PMID: 17396127).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DsRED labeled carcinoma cell lines and GFP expressing primary CAFs were cultured either separately or in co-cultures for 17 hours. Colonies were released from Matrigel by 30 min incubation in PBS/EDTA, at which point separately cultured cells were combined to control for cross-contamination. Cell mixtures were washed with PBS, trypsinized for 7 min, quenched with serum containing media, washed and spun down. Epithelial cells were selected using Epithelial Enrich dynabeads (Life Technologies) following manufacturer’s protocol. Microscopic examination of captured cells revealed no detectable CAF contamination.
From each sample 5E5 cells were used to prepare SAGE-Seq (serial analysis of gene expression combined with the Illumina/Solexa 1G platform) libraries according to a detailed protocol available at http://polyaklab.dfci.harvard.edu/index.php/science/protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
cultured separately
|
| Data processing |
Library strategy: SAGE-Seq
SAGE-Seq: Basecalls were performed using CASAVA version 1.8.2
SAGE-Seq: The sequencing tags were mapped and normalized as described in Wu et al., Genome Research, 2010 (PMID: 21045080). Tag counts used were the sums of all sense SAGE-Seq tags uniquely mapped to the same gene.
processed data files format and content: SAGE-Seq: Tab-separated file of the normalized tag 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 |
GPL16791 |
| Series (1) |
| GSE80333 |
Spatial proximity to fibroblasts impacts molecular features and therapeutic sensitivity of breast cancer cells influencing clinical outcomes |
|
| Relations |
| BioSample |
SAMN04858676 |
| SRA |
SRX1707750 |
