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| Status |
Public on Sep 05, 2022 |
| Title |
GS3-PDX092 |
| Sample type |
SRA |
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| Source name |
breast cancer PDX model, Treat2, replicate 1
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| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer PDX
treatment: Treat2 (E2, 10 days)
run: run 1
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| Treatment protocol |
After tumor volume reached approximately 200mm3, mice were randomized and implanted with an Placebo or E2 (1mg) pellet on their backside. These treatments lasted 5/10/53 days for experiments on RNA sequencing analysis.
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| Growth protocol |
Surgically resected brain metastasis tumor pieces were implanted into the 4th mammary fat pat of female NOD-scid/IL2Rγ-/- (NSG) mice, that were 6-8 weeks old, to establish PDX lines.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from GS3 tumors were extracted using the RNeasy Plus Mini Kit (Qiagen)
RiboZero Stranded mRNA-Seq Kit; stranded ribosome-depletion RNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ribosome-depleted,stranded
RNA-Seq data, Treat2, PDX model, replicate 1
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| Data processing |
Real Time Analysis (RTA, v1.18.64) was used for base calling, and bcl2fastq was used to generate FASTQ files (v1.8.4 for samples 1-6 in run 1, and v2.18 for samples 7-8 in run 2)
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search --library-type fr-firststrand
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016).
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count)
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| Submission date |
Aug 26, 2020 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Shiuan Chen |
| E-mail(s) |
[email protected]
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| Organization name |
City of Hope National Medical Center
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| Department |
Cancer Biology-BRI
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| Street address |
1500 E Duarte Rd
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| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE156922 |
Estrogen-induced cell cycle arrest in patient-derived xenograft (PDX) modal for breast cancer |
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| Relations |
| BioSample |
SAMN15914243 |
| Supplementary data files not provided |
| Processed data are available on Series record |
| Raw data not provided for this record |
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