|
| Status |
Public on Jun 28, 2024 |
| Title |
68H_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Brx68
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Brx68
cell type: patient derived CTC line
treatment: Hypoxia
|
| Growth protocol |
CTC lines derived from patients with luminal breast tumors were cultured in ultra-low attachment plates (Corning) with RPMI 1640 supplemented with 20 ng/ml EGF, 20 ng/ml bFGF, 1X B27 and 1X antibiotic/antimycotic. CTCs were maintained in a Nuaire NU-5831 incubator at 4% O2 and 5% CO2, and media was changed every 3 or 4 days in regular cell culture hood in ambient oxygen. For normoxia vs hypoxia experiments, equal number of cells were plated and kept in normoxia or hypoxia (4% O2) conditions for 8 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected into tubes containing PBS, centrifuged and lysed with Quick RNA lysis buffer to proceed with RNA extraction with Quick-RNA MicroPrep (Zymo) according to the manufacturer’s instructions. RNA integrity was measured using Bioanalyzer (Agilent).
Sequencing libraries were prepared with KAPA stranded RNA-Seq Kit with RiboErase (Kapa Biosystems) according to manufacturer’s instructions, and single-end 75 bp sequencing was performed at the USC Molecular Genomics Core, using a NextSeq high output 75 cycle kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
hypoxia 8 weeks
|
| Data processing |
Reads were trimmed for Nextera and Illumina adapter sequences using trimgalore with default parameters. Trimmed reads were mapped to hg19 (GRCh37) reference using STAR (v2.7.1a), and the reads mapped to the genes annotated in the ENSEMBL GRCh37.p13 GTF (release 75) were quantified using HTSeq-count (v0.11.2). Differentially expressed genes across hypoxia-normoxia conditions were identified after controlling for cell line and batch effects (FDR≤0.05), using DESeq2 (v1.26.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text files with raw counts
|
| |
|
| Submission date |
Jun 16, 2024 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Christopher Russell Chin |
| E-mail(s) |
[email protected]
|
| Phone |
3393640514
|
| Organization name |
Weill Cornell
|
| Lab |
Melnick Lab
|
| Street address |
413 E 69th Street, Belfer Building, BB-1462
|
| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE269984 |
Hypoxic Memory Mediates Prolonged Tumor Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression [RNA-Seq] |
| GSE270903 |
Hypoxic Memory Mediates Prolonged Tumor Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression |
|
| Relations |
| BioSample |
SAMN41860026 |
| SRA |
SRX24941879 |
