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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 08, 2020 |
| Title |
PJ_2-C2 |
| Sample type |
SRA |
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| Source name |
breast cancer cells SUM159
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159
treatment: JQ1+palbociclib
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| 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, or for 1 week with JQ1 followed by 1 week with paclitaxel, 1 week with paclitaxel followed by 1 week with JQ1, or 1 week with JQ1+paclitaxel followed by 1 week with vehicle, with 5 mice per group.
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| 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.
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| 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). Equal amounts of DNA were pooled from replicates for library construction.
DNA was fragmented to 250 bp (Covaris ultrasonication) and further purified using Agencourt AMPure XP beads. Size-selected DNA was ligated to sequencing adaptors with sample-specific barcodes using the KAPA Hyper Prep Kit. Libraries were pooled and sequenced on an Illumina MiSeq nano flow cell to estimate the library DNA concentration based on the number of barcode reads per sample. Libraries were pooled and captured using SureSelectXT Human All Exon v5 (Agilent) in 7 x 3-plex and 1 x 2-plex. Captures were performed using the SureSelectXT Reagent Kit (Agilent).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
experiment: JQ1+palbociclib in vitro
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| Data processing |
Library strategy: Exome-Seq
Alignment using Picard (http://broadinstitute.github.io/picard)
SNV calling using MuTect v1.1.4 (Cibulskis et al., 2013) and annotation using Varient Effect Predictor (VEP, McLaren et al., 2010). MuTect was run in paired mode pairing the tumor samples to the project normal, CEPH 1408.
Indel calling using GATK
Variant annotation using OncoAnnotate
CNV calling using RobustCNV. RobustCNV relies on localized changes in mapping depth of sequenced reads in order to identify changes in copy number. Observed values are normalized against the mapping depth in a panel of normals (PON) sampled with the same capture bait set. Normalized coverage data are then segmented using Circular Binary Segmentation (Olshen et al., 2004) with the DNAcopy Bioconductor package. Finally, segments are assigned gain, loss, or normal-copy calls using a cutoff derived from the within-segment standard deviation and a tuning parameter set based on comparisons to array-CGH calls in separate validation experiments.
Genome_build: b37
Supplementary_files_format_and_content: SNV and indel report contains variants with genomic coordinates, gene, DNA and protein change, allele fraction, coverage, and annotations from dbSNP, COSMIC, and gnomAD. CNV report contains gene level calls, with genomic coordinates and coverage levels, and chromosome arm-level calls.
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| Submission date |
May 30, 2019 |
| Last update date |
Apr 08, 2020 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
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| Phone |
617-632-2106
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| Organization name |
Dana-Farber Cancer Institute
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| Department |
Medical Oncology
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| Lab |
Polyak
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| Street address |
450 Brookline Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (2) |
| GSE131980 |
Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer [Exome] |
| GSE131986 |
Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer |
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| Relations |
| BioSample |
SAMN11895353 |
| SRA |
SRX5935770 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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