|
Status |
Public on Sep 28, 2016 |
Title |
Breast_Normal_Fibroblast_2 |
Sample type |
SRA |
|
|
Source name |
Fibroblast from normal breast tissue
|
Organism |
Homo sapiens |
Characteristics |
tissue of origin: breast (normal)
|
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
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|
|
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 |
SAMN04858688 |
SRA |
SRX1707762 |