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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jan 07, 2022 |
Title |
T_MC38_Baseline_3 |
Sample type |
SRA |
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Source name |
Tumor
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Organism |
Mus musculus |
Characteristics |
replicate group: T_MC38_Baseline treatment: none cell line: MC38 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-1377691
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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 |
SAMN18296229 |
SRA |
SRX10336960 |
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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