|
| Status |
Public on Apr 22, 2024 |
| Title |
Group-03-180-PanO2 |
| Sample type |
SRA |
| |
|
| Source name |
Subcutaneous Pan02 tumors
|
| Organism |
Mus musculus |
| Characteristics |
group: Group-03
animal id: 180
treatment: BXCL701
dose level (mg/kg): 20 ug/ mouse
dosing frequency & duration: Single dose
harvest time (day/h): Day1 / 8hr
|
| Treatment protocol |
Cells were injected into the right flank of C57BL/6J or Balb/c wild-type mice. Mice were given either 20 ug BXCL701 daily by oral gavage or 200ug of anti-PD1 (clone: RMP1-14, BioXcell) twice per week by intraperitoneal (i.p.) injection or both.
|
| Growth protocol |
Mice were euthanized at end of treatment or when tumors reached 1-2 cm3 for mT3-2D tumors or 3 cm3 for other tumors or when mice showed signs of pain or distress, via CO2 inhalation. Volume was calculated using (length × width 2)/2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Subcutaneous Pan02 tumors were collected in RNAlater after 1, 7 or 14 days of BXCL701 or PBS treatment. RNA was extracted from each sample using RNeasy mini kit (QAIGEN, Cat. 74106).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The adapter and low quality sequences were trimmed by Trimmomatic-0.36 software.
The reads from the clean data after trimming were mapped to reference genes (ENSEMBL GRCm38.84) by Bowtie-0.12.9 software
The gene expression was calculated by MMSEQ_1.0.2 software.
Genome_build: ESEMBL GRCm38.84
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and sample
|
| |
|
| Submission date |
Apr 27, 2021 |
| Last update date |
Apr 22, 2024 |
| Contact name |
Elana Judith Fertig |
| E-mail(s) |
ejfertig@jhmi.edu
|
| Organization name |
Johns Hopkins University
|
| Department |
Oncology Quantitative Sciences
|
| Street address |
550 N Broadway, Suite 1101E
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21209 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE173441 |
Exploring the effects of DPP inhibition on the tumor immune landscape using RNAseq |
|
| Relations |
| BioSample |
SAMN18882433 |
| SRA |
SRX10690796 |
