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Sample GSM4301286 Query DataSets for GSM4301286
Status Public on Jun 01, 2020
Title M1 GEM-derived allograft
Sample type SRA
 
Source name Melanoma allograft
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: BrafCA/+; Ptenflox/+; Cdkn2aflox/+; Tyr-CreERT2-tg
treatment: Untreated
Extracted molecule genomic DNA
Extraction protocol Cell lines were harvested following regular cell culture process. Tumors harvested from mice were homogenized by cryogenic grinding. Genomic DNA and RNA was prepared using Qiagen DNeasy Blood & Tissue Kit and RNeasy Blood & Tissue Kit, respectvely.
Exome and cDNA (RNA) libraries were prepared for sequencing using Agilent SureSelectXT library prep ILM Kit and standard Illumina library prep, respectively.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Data processing Library strategy: Exome-seq
Quality checking (trimming/masking if necessary), alignment/mapping to the reference genome; Variant calling (SNVs and indels) and comparisons between the conditions; IGV visualizations.
Using combination of Galaxy on Helix and Bioconductor /R packages
Single nucleotide variants (SNV) were identified using samtools mpileup or GATK HaplotypeCaller. Mouse germline single nucleotide polymorphisms (SNPs) were filtered out using the Sanger Mouse Genomes Project database
Variants with a Phred-scaled quality score of <30 were removed. Variants that are present in normal spleen samples (in-house collection) were also removed.
Variants were annotated with Annovar software to identify non-synonymous mutations.
Genome_build: UCSC reference Genome Sequence, mouse mm10
Supplementary_files_format_and_content: vcf files include variants for each sample
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …
 
Submission date Feb 07, 2020
Last update date Jun 01, 2020
Contact name Maxwell Lee
E-mail(s) leemax@mail.nih.gov
Phone 240-276-5239
Organization name National Cancer Institute, NIH
Department CCR
Lab Laboratory of Human Carcinogenesis
Street address Building 37, Room 5120
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL21493
Series (1)
GSE144946 Multi-model preclinical platform predicts clinical response of melanoma to immunotherapy
Relations
BioSample SAMN14057169
SRA SRX7692455

Supplementary file Size Download File type/resource
GSM4301286_EPG_3.vcf.gz 6.5 Mb (ftp)(http) VCF
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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