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Sample GSM7791010 Query DataSets for GSM7791010
Status Public on Feb 06, 2024
Title YU-003 PDX, residual, rep3
Sample type SRA
Source name Patient-derived xenograft
Organism Homo sapiens
Characteristics tissue: Patient-derived xenograft
treatment: Osimertinib for 6 weeks
Treatment protocol Mice were treated with with osimertinib at 25mg/kg for five consecutive days each week. The treatment lasted for 6 weeks before drug tolerant residual tumor was excised.
Growth protocol Dissociated PDX tissues were implanted subcutaneously into NSG mice. Treatment was started as the tumors grew to appropriate size.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from tissue powder using AllPrep DNA/RNA mini kit (Qiagen, 80204).
RNA-seq libraries were constructed using KAPA mRNA HyperPrep Kit (Kapa Biosystems, KR1352).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description Y5751
Data processing Sequencing reads were trimmed of adaptor sequences using Trim Galore.
Reads were mapped to a combined human (hg38) and mouse (mm10) genome using STAR to separate the components of the two species and to a combined transcriptome (GENCODE v24 for human, vM10 for mouse) to add gene annotation.
The uniquely mapped reads were counted per annotation using featureCounts.
The counting matrix went through DESeq2 package to identify the genes that are differentially expressed between different conditions.
Assembly: Hybrid human (hg38) and mouse (mm10) genome
Supplementary files format and content: csv files including RPKM values for each gene in different PDXs
Submission date Sep 19, 2023
Last update date Feb 06, 2024
Contact name Bomiao Hu
Organization name Yale University
Street address 310 Cedar Street
City New Haven
State/province CT
ZIP/Postal code 06519
Country USA
Platform ID GPL16791
Series (2)
GSE243564 ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts [PDX RNA-seq]
GSE243569 ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts
BioSample SAMN37473051
SRA SRX21829185

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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