|
| Status |
Public on Nov 02, 2023 |
| Title |
Nko2_1 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Melanoma cell line
cell line: B16F10
cell type: Melanoma
genotype: NGF-/-
treatment: Total RNA from melanoma cells
|
| Treatment protocol |
CRISPR/Cas9 technology was used to generate NGF knockout stable cell lines.
|
| Growth protocol |
B16F10 cells were subcutaneously injected into C57BL/6J mice. Total RNA was extracted from melanoma tissues on day 15 and analyzed by RNA-seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extrated using a kit from ZYMO RESEARCH (Direct-zol RNA miniprep, cat. No. R2052) according to the manufacturer’s instructions and dissolved in RNase-free water.
Sequencing libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol. Libraries were sequenced using an Illumina HiSeq machine and paired-end reads were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads with default parameter. Only bases with quality ≥20 and only reads that were ≥20nt after trimming were kept for further analysis.
Reads were mapped to mouse genome reference combining the GRCm38. STAR software was used to align reads to reference genome. Reads were kept for subsequent analysis if they mapped to a single genomic location. Reads with mappiing quality <20 were excluded. Gene counts were measured using the featureCounts.
Assembly: GRCm38
Supplementary files format and content: Tao_NGF_featurecount_matrix.txt: Reads mapped to human GRCm38, featurecount was used to count reads per gene per sample, tab-delimited txt file
|
| |
|
| Submission date |
Jul 06, 2023 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Liuyang Wang |
| Organization name |
Duke University
|
| Street address |
213 Research Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE236673 |
Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection [RNA-Seq 1] |
| GSE236682 |
Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection |
|
| Relations |
| BioSample |
SAMN36345324 |
| SRA |
SRX20928450 |
