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Sample GSM5437376 Query DataSets for GSM5437376
Status Public on Oct 06, 2021
Title MC38_tumor_HFD
Sample type SRA
 
Source name Mouse xenograft models
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: male
diet: 45% fat
tissue: tumor
Treatment protocol Following 28 weeks of diet treatment mice were injected subcutaneously with 2x105 MC38 cells. Tumors were collected on Day 20 post injection and mechanically and enzymatically digested using miltenyi mouse tumor digestion kit following manufacturer’s instructions. CD45+ cells were separated from tumor suspensions using CD45+ microbeads (miltenyi) and enriched for live cells using a dead cell removal kit (miltenyi). Three samples from each diet treatment group were resuspended in PBS + 0.4% FBS and pooled together in equal number of live cells prior to submitting to single cell sequencing. Cell viability for all samples were >95% via trypan blue prior to submission
Growth protocol 8-week-old C57BL/6 male mice were fed ad libitum a 10% kcal from fat (low fat) diet or a 45% kcal fat (high fat) diet (Research Diets D12450H and D12451, respectively).
Extracted molecule total RNA
Extraction protocol 10X Single Cell 5' PE; mRNA 5' capture
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 4834-JB-3_S01_L005
Data processing cellranger-4.0.0
scanpy-1.7.1
Genome_build: mm10
Supplementary_files_format_and_content: formatted hdf5 file containing mnn integrated matrix
 
Submission date Jul 12, 2021
Last update date Oct 06, 2021
Contact name John Karijolich
E-mail(s) john.karijolich@vumc.org
Organization name Vanderbilt University Medical Center
Department PMI
Lab John Karijolich Lab
Street address 1211 Medical Center Drive
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL24247
Series (1)
GSE179936 Single Cell RNA Sequencing reveals heterogenous tumor associated immune cell compartment in lean vs obese mice using an MC38 tumor model
Relations
BioSample SAMN20172563
SRA SRX11412312

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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