|
| Status |
Public on Jul 18, 2023 |
| Title |
BCM-5097_107348 |
| Sample type |
SRA |
| |
|
| Source name |
ER+ breast cancer patient-derived xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
biomaterial provider: Baylor College of Medicine
cell type: PDX
treatment: Estrogen pellet
tissue: PDX mammary tumor
|
| Treatment protocol |
Carboplatin Resistant: Mice with PDXs were grown and treated three times spaced out every 4 days with 40mg/kg of carboplatin. Once the tumors regrew they were passaged to new recipient mice and then treated with another set of carboplatin. This proceeded until the tumors no longer responded to carboplatin; at this point they were termed carboplatin-resistant.
Tamoxifen Resistant: Mice harboring PDX tumors were given tamoxifen citrate chow. These PDXs were passaged under tamoxifen citrate selection until no difference in growth rate between treated and untreated tumors was observed. These models were then termed "tamoxifen resistant."
Tamoxifen citrate: Chow was replaced with Tamoxifen citrate chow from Envigo (600mg/kg) for 2 weeks prior to tumor excision.
Estradiol Withdrawal (EWD): Ovariectomy was performed and no exogenous estrogen pellet was provided.
Estrogen pellet:Two milligram slow-release estrogen pellets were implanted subcutaneously as an exogenous source of estrogen.
Ovariectomy (OVX): Both ovaries were surgically removed from mice to withdraw the primary source of estrogen.
|
| Growth protocol |
PDX tumors were grown orthotopically in NSG mice for 8 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10x Genomics Chromium kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Basecalling: BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14)
QC: Fastq files containing the read were analyzed with FastQC v.0.11.8 to identify any quality concerns with the raw data.
Alignment: Fastq files were aligned independently to the merged human/mouse hg19mm10 genome provided by 10X using CellRanger v6 "count" algorithm with the expected number of cells set to 5000.
Mouse Cell Removal: An in-house R script and the 10X-generated GEM file were used to identify and remove all mouse and multiplet cell barcodes from each PDX sample by using the CellRanger script "subset_bam". The remaining reads were converted back to fastq files using the CellRanger script "bamtofastq". These new filtered fastq files were then re-aligned independently to the GRCh38 human genome using the CellRanger "count" algorithm, however, this time the Force Cells option was set to the exact number of remaining human cells for each sample.
Dead Cell Removal: An in-house R script using the Seurat v4 R package was used to identify and remove barcodes associated with dead or poor quality cells. The 10X "subset_bam" and "bamtofastq" scripte were once again used to filter the bam files for each sample to generate fastq files containing only the reads from good quality human cells.
Alignment: Each sample was re-aligned to the human GRCh38 genome provided by 10X using the CellRanger "count" algorithm with the Force Cells option set to the exact number of good quality cells identified in the previous step.
Assembly: GRCh38
Supplementary files format and content: The process data files include the 10X formatted features.tsv.gz, barcodes.tsv.gz, and matrix.mtx.gz files that can be imported directly into R using the Seurat package.
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Jul 18, 2023 |
| Contact name |
Wright Center for Clinical and Translational Research Bioinformatics Core |
| E-mail(s) |
cctrbioinfo@vcu.edu
|
| Phone |
804-828-1621
|
| Organization name |
Virginia Commonwealth University
|
| Street address |
203 E Cary St
|
| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE235168 |
Evaluation of breast cancer PDX tumor heterogeneity at single cell resolution [scRNA-seq] |
| GSE235169 |
Evaluation of breast cancer PDX tumor heterogeneity |
|
| Relations |
| BioSample |
SAMN35801811 |
| SRA |
SRX20726552 |
