|
| Status |
Public on Jun 01, 2020 |
| Title |
M1 Cell line-derived allograft Isotype control A88 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma allograft
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: BrafCA/+; Ptenflox/+; Cdkn2aflox/+; Tyr-CreERT2-tg
treatment: Isotype control
|
| 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 |
SAMN14057158 |
| SRA |
SRX7692465 |
