|
| Status |
Public on Sep 24, 2019 |
| Title |
sample_1_L001 |
| Sample type |
SRA |
| |
|
| Source name |
Lung to brain metastasis cells
|
| Organism |
Homo sapiens |
| Characteristics |
bmic line: 478
stage of the metastatic cascade: original
biological sample id: Sample 1
|
| Growth protocol |
Brain metastases (BM) originating from non-small cell lung carcinoma (NSCLC) primary samples were processed and maintained in Neurocult media (STEMcell Technolgies) as brain metastasis initiating cells (BMICs). BMICs were grown as tumorspheres that were maintained at 37°C with a humidified atmosphere of 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from BMICs using Norgen total RNA kit.
Library prep was performed using the NEBNext Ultra Directional RNA Library Prep Kit along with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were subject to further BioAnalyzer QC and quantified by qPCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Replicate 1
|
| Data processing |
Raw RNA sequencing data were preprocessed and normalized as follows:
RNAseq data were aligned against hg38 reference genome, using bowtie2.
Reads counts per gene were obtained using R packages GenomicRange and GenomicFeatures and using UCSC hg38 KnowGene database as a reference for genomic locations (TxDb.Hsapiens.UCSC.hg38)
Counts were normalized to counts per million.
Additional quantile normalization was applied.
Genome_build: HG38 (TxDb.Hsapiens.UCSC.hg38)
Supplementary_files_format_and_content: Entrez ID, Gene Symbol, Counts per millions as obtained across samples and their replicates
|
| |
|
| Submission date |
Feb 12, 2018 |
| Last update date |
Sep 24, 2019 |
| Contact name |
Igor Jurisica |
| E-mail(s) |
juris@ai.utoronto.ca
|
| Phone |
4165817437
|
| Organization name |
University Health Network
|
| Department |
Krembil Research Institute
|
| Lab |
Jurisica Lab
|
| Street address |
60 Leonard Avenue
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5T2S8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE110495 |
Therapeutic targeting of the pre-metastatic stage in human brain metastasis |
|
| Relations |
| BioSample |
SAMN08519427 |
| SRA |
SRX3683662 |
