|
Status |
Public on Feb 06, 2024 |
Title |
YU-006 PDX, untreated, rep2 |
Sample type |
SRA |
|
|
Source name |
Patient-derived xenograft
|
Organism |
Homo sapiens |
Characteristics |
tissue: Patient-derived xenograft treatment: Untreated
|
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 |
Y7159
|
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 |
E-mail(s) |
bomiao.hu@yale.edu
|
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 |
|
Relations |
BioSample |
SAMN37473049 |
SRA |
SRX21829187 |