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| Status |
Public on Jul 18, 2023 |
| Title |
WHIM30-107658 |
| Sample type |
SRA |
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| Source name |
Basal-like triple-negative breast cancer patient-derived xenograft
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
biomaterial provider: Washington University in St. Louis
cell type: PDX
treatment: 100mg/kg byl-719 gavage
tissue: PDX mammary tumor
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| 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.
BYL-719: 50-100mg/kg daily
Carboplatin: 40mg/kg 3 doses spaced every 4 days
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| Growth protocol |
PDX tumors were grown orthotopically in NSG mice for 8 weeks.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy
Library construction protocol: The RNA sample received was quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
WHIM30-107658
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| 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: STAR v2.5.2b was used for alignment with the following settings: --outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1
Read Counting: Salmon v0.8.2 was used for counting reads with the "quant" algorithm and library type set to "IU" using the transcriptome output of STAR.
Assembly: A custom reference genome was built by concatenating the following three genome builds: GRCh38 human genome from the Genomic Data Commons (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files), GRCm38 M12 Gencode release of the Mouse genome (http://www.gencodegenes.org/mouse_releases/12.html), and the Xenotropic murine leukemia virus accession JF274252.1 (https://www.ncbi.nlm.nih.gov/nuccore/JF274252.1). Prior to concatenation, human chromosomes were concatenated with "HUMAN_" and mouse chromosomes were concatenated with "MOUSE_".
Supplementary files format and content: The processed data files contain the output from Salmon and include Salmon calculated TPM, gene lengths, and raw counts for the human and mouse genomes.
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| Submission date |
Jun 16, 2023 |
| Last update date |
Jul 18, 2023 |
| Contact name |
Wright Center for Clinical and Translational Research Bioinformatics Core |
| E-mail(s) |
cctrbioinfo@vcu.edu
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| Phone |
804-828-1621
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| Organization name |
Virginia Commonwealth University
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| Street address |
203 E Cary St
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| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
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| Platform ID |
GPL25431 |
| Series (2) |
| GSE235167 |
Establishment of breast cancer PDX RNA-sequencing data library [bulk RNA-seq] |
| GSE235169 |
Evaluation of breast cancer PDX tumor heterogeneity |
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| Relations |
| BioSample |
SAMN35778126 |
| SRA |
SRX20710189 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7496257_WHIM30-107658_001.trimmed.quant.sf.gz |
3.9 Mb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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