|
| Status |
Public on Jul 05, 2022 |
| Title |
Cancer rep1 |
| Sample type |
SRA |
| |
|
| Source name |
breast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endothelial cells
tissue: primary tumor
|
| Growth protocol |
The samples of healthy tissue and primary breast tumor were obtained from the same patient and were seeded at density 5x10^4 cells/10cm^2. Both endothelial cell lines were cultured on Primaria Tissue Culture Flask (Corning #353808) in the presence of Opti-MEM I Reduced Serum Medium (Gibco #31985070) supplemented with 2% (vol/vol) fetal bovine serum (Gibco #A3840402). All cells were maintained at 37°C and 5% CO2 in humidified atmosphere. Lastly, to experiments cells were detached with enzyme cell detachment medium: Accutase supplied in Dulbecco's PBS containing 0.5 mM EDTA and phenol red (Invitrogen #E136579). The cell lines were mycoplasma free (PromoKine #PK-CA91-1096).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the cell cultured upon normoxia for 48h, accordingly to manufacturer’s protocol with RNeasy Plus Mini Kit (Qiagen #74136)
Libraries were prepared with the NEBNext Library Prep Kit (BioLabs #E7770S)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
raw_counts_HN_CaN.txt
9_2CaN
|
| Data processing |
Single-end reads were aligned to Ensembl GRCh38 himan genome with STAR (v2.7)
Counts were obtained using featureCounts v1.6.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Jul 05, 2022 |
| Contact name |
Klaudia Brodaczewska |
| E-mail(s) |
kbrodaczewska@wim.mil.pl
|
| Organization name |
Military Institute of Medicine
|
| Street address |
Szaserow 128
|
| City |
Warsaw |
| ZIP/Postal code |
04-141 |
| Country |
Poland |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE179509 |
Distinctive properties of endothelial cells from tumor and normal tissue in human breast cancer |
|
| Relations |
| BioSample |
SAMN20079270 |
| SRA |
SRX11359484 |
