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Sample GSM4301334 Query DataSets for GSM4301334
Status Public on Jun 01, 2020
Title M4 Cell line-derived allograft anti-CTLA4 C54
Sample type SRA
 
Source name Melanoma allograft
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Hgftg
treatment: anti-CTLA4
Extracted molecule total RNA
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description GEO_GlennRNAseq46_rpkm
Data processing 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 SAMN14057235
SRA SRX7692504

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

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