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SRX20710229: GSM7496289: HCI-001CR7-107992; Homo sapiens; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 29.8M spots, 8.9G bases, 2.8Gb downloads

External Id: GSM7496289_r1
Submitted by: Virginia Commonwealth University
Study: Establishment of breast cancer PDX RNA-sequencing data library [bulk RNA-seq]
show Abstracthide Abstract
Breast cancer is the most commonly diagnosed cancer among women. PDXs (patient-derived xenografts) are similar to cancer cell lines but differ in that they are maintained in a physiological setting as soon as they are isolated from the patient and for subsequent passages. These models are valuable for preclinical trials because PDX models have been shown to closely match their patient counterparts, both in genomic profile and response to treatment. Collection of RNA-expression data from multiple PDX models was performed to generate a library of RNA-sequencing data which may be utilized to compare tumors from different subtypes or treatment groups. Overall design: ER+ and triple negative mammary tumors were grown orthopedically in mice for 8 weeks. Tumor cells from each PDX were profiled by bulk RNA-sequencing to determine differentially expressed genes and gene signatures between models with the goal of furthering the fields of oncogenesis, metastasis and drug resistance.
Sample: HCI-001CR7-107992
SAMN35778094 • SRS18002977 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM7496289
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction 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).
Runs: 1 run, 29.8M spots, 8.9G bases, 2.8Gb
Run# of Spots# of BasesSizePublished
SRR2495216729,828,6158.9G2.8Gb2023-07-18

ID:
28140259

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