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| Status |
Public on May 20, 2024 |
| Title |
DNA, 1956 cells |
| Sample type |
SRA |
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| Source name |
In vitro cultured cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: In vitro cultured cells
cell line: 1956
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA and RNA were isolated from in vitro cultured 1956 and F244 cells using QIAamp DNA Kits (Qiagen, Cat# 56304) and RNeasy Kits (Qiagen, Cat# 74104), respectively, according to manufacturer’s instructions. DNA was isolated from tails of female C57BL/6N and male 129S6 mice to serve as control for 1956 and F244, respectively.
Exome sequencing libraries were generated using the NEBNext Ultra II FS Kit (NEB, Cat# E7805). Tumor RNA was subjected to DNase treatment and ribodepletion prior to library construction using NEBNext Ultra II Directional RNA library prep kit for Illumina (NEB, Cat# E7760).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Mutation_1956.vcf
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| Data processing |
For whole exome sequencing, paired-end 151 base pair reads were sequenced on the NovaSeq6000 to aim for 100x coverage in normal and 250x in tumor samples. For RNA-seq, paired-end 151 base pair reads were generated on the NovaSeq6000 to generate for a minimum of 80 million reads per sample; reads were aligned to the mouse genome reference sequence build GRCm38. Alignment was performed using a custom in-house pipeline and the splice-aware aligner STAR (RRID_SCR_004463). The Salmon tool (RRID:SCR_017036) was used to quantify transcript abundance from the tumor RNA-seq reads generated.
Assembly: mm9
Supplementary files format and content: Tab-delimited text file contains mutation data
Supplementary files format and content: Excel file contains TPM values for F244 and 1956 lines
Library strategy: Whole exome sequencing
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| Submission date |
May 20, 2024 |
| Last update date |
May 20, 2024 |
| Contact name |
Robert D Schreiber |
| Organization name |
Washington University in St. Louis
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| Department |
Department of Pathology and Immunology
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| Street address |
425 South Euclid
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| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE267886 |
Neoantigen identification for 1956 and F244 murine MCA-sarcomas |
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| Relations |
| BioSample |
SAMN41464454 |
| SRA |
SRX24614676 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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