|
| Status |
Public on Apr 08, 2020 |
| Title |
JP_DMSO_P2_1 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cells SUM159
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159
treatment: DMSO
time point: passage 2
replicate: 1
|
| Treatment protocol |
Cells were grown in vitro in the presence of DMSO, JQ1 (100 nM), paclitaxel (0.6 nM), palbociclib (160 nM), JQ1+paclitaxel, or JQ1+palbociclib, in triplicates, for up to 18 passages. Mice were treated for up to 2 weeks with vehicle, JQ1 (30-50 mg/kg daily), palbociclib (75 mg/kg daily), paclitaxel (10 mg/kg twice weekly), JQ1+palbociclib, or JQ1+paclitaxel, with 5 mice per group.
|
| Growth protocol |
Cells were lentivirally infected with the ClonTracer barcode library (Bhang et al., 2015). Barcoded cells were passaged in vitro in the presence of drug or injected orthotopically into mammary fat pads of NOG mice to produce xenografts.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from frozen cultured cells and xenografts using the AllPrep DNA/RNA Mini Kit or the QIAamp DNA Mini Kit (Qiagen).
PCR was used to amplify barcodes and introduce Illumina adaptors along with a 5 bp index sequence for multiplexing as described (Bhang et al., 2015). 2 µg of genomic DNA was used as template, and 15-16 samples were multiplexed. PCR products were run on 0.8% agarose NGS E-Gels (Invitrogen) to verify the correct library size, and bands were purified using the MinElute Gel Extraction Kit (Qiagen).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
experiment: JQ1+palbociclib in vitro
|
| Data processing |
Remove 3' adapter and discard reads shorter than 30 bp using fastx_clipper
Filter for reads matching the barcode pattern (alternating A/T and C/G) and with a Phred quality score of at least 10 for all base pairs and an average Phred score of 30
Genome_build: N/A
Supplementary_files_format_and_content: TSV files contain unique barcode sequences with corresponding number of reads.
|
| |
|
| Submission date |
May 30, 2019 |
| Last update date |
Apr 08, 2020 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| Phone |
617-632-2106
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Polyak
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE131977 |
Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer [Barcode] |
| GSE131986 |
Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer |
|
| Relations |
| BioSample |
SAMN11894667 |
| SRA |
SRX5935643 |
