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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 07, 2022 |
| Title |
T_MBT2_Baseline_1 |
| Sample type |
SRA |
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| Source name |
Tumor
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| Organism |
Mus musculus |
| Characteristics |
replicate group: T_MBT2_Baseline
treatment: none
cell line: MBT2
pd1responder: High
time point: Baseline
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| Treatment protocol |
Tumor-bearing mice received muDX400, or muIgG1 isotype control, antibody injection at day 11 and day 15 post-tumor implant. Subsequently, on day 19 (“8d”) tumors were excised and snap frozen in liquid nitrogen and stored at –80°C until RNA isolation.
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| Growth protocol |
Each mouse was anesthetized and inoculated subcutaneously into the right lower flank with a single-cell suspension of ≥95% viable cells in 0.1 mL of serum-free DMEM or RPMI-1640 medium. Mice were checked daily for signs of notable clinical observations.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For tumor tissue RNA isolation, organs were homogenized into RNA STAT-60 (Tel-Test Inc., Friendswood, TX) using a polytron homogenizer, then total RNA extracted according to the manufacturer's instructions. After isopropanol precipitation, total RNA was re-extracted with phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma-Aldrich, St. Louis, MO) using phase-lock light tubes (Thermo Fisher Scientific, Foster City, CA).
RNA sequencing was performed using the Truseq stranded total RNA RiboZero library preparation kit (Catalog #: RS-122-2201) according to the manufacturer’s instructions (Illumina, San Diego, CA). The resulting cDNA libraries were sequenced on Illumina HiSeqTM 4000 using a 50 base paired-end run.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
US-1377625
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| Data processing |
Cleaned reads were aligned to the Mouse.B38 genome reference using the Omicsoft Aligner (Qiagen, Germantown, MD) with a maximum of 2 allowed mismatches.
Gene level raw counts, and FPKM, were determined by the OSA algorithm as implemented in Omicsoft Array Studio (version 10.0.1.118) and using Ensembl.R93 gene models.
Genome_build: Mouse.B38
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample. Each column corresponds to one sample (barcode).
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| Submission date |
Mar 13, 2021 |
| Last update date |
Jan 07, 2022 |
| Contact name |
Eric Muise |
| E-mail(s) |
eric_muise@merck.com
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| Phone |
6179923514
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| Organization name |
Merck
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| Department |
GPGX
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| Street address |
33 Ave. Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE168846 |
Molecular Determinants of Response to Anti–PD-1 Immunotherapy in Syngeneic Tumor Mouse Models |
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| Relations |
| BioSample |
SAMN18296170 |
| SRA |
SRX10336943 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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