|
| Status |
Public on Jun 19, 2024 |
| Title |
B16_TdgKO1 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cell line
cell line: B16
cell type: Melanoma
genotype: Tdg KO
|
| Growth protocol |
KP and B16 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol reagent (Invitrogen).
1 μg total RNA was used for the following library preparation. RNAseq libraries were prepared with VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611). The poly(A) mRNA isolation was performed using Oligo(dT) beads. Using divalent cations and high temperatures, mRNA fragmentation was achieved and the priming process was carried out using random primers. Then first strand cDNA and the second-strand cDNA were synthesized. Once the double-stranded cDNA was purified, adaptors were added to both ends after end repair and dA-tailing. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Libraries were finally subjected to 150 bp paired-end sequencing using the Illumina NovaSeq 6000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
B16_raw_counts.csv
|
| Data processing |
Raw data were trimmed by Trim Galore (v0.6.6) with default settings. Then, the clean data were mapped to mouse reference genome mm10 using Hisat2 (v2.1.0) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Gene count matriceswere calculated by featureCounts (v1.6.4) with the parameters -p -M -O. Differentially expressed gene (DEG) analysis was performed by using DESeq2 package. Only genes with adjusted P value < 0.05 and fold change > 2 were considered to be differentially expressed. DEGs were submitted to DAVID (2021 Update) (https://david.ncifcrf.gov/) for gene ontology (GO) and KEGG pathway enrichment analyses. GSEA was performed using clusterProfiler package.
Assembly: mm10
Supplementary files format and content: comma-separated values file, raw counts for gene expression.
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| |
|
| Submission date |
Jul 06, 2023 |
| Last update date |
Jun 19, 2024 |
| Contact name |
Zhenyu Shao |
| Organization name |
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
|
| Department |
Center for Excellence in Molecular Cell Science
|
| Street address |
Yueyang Road 320
|
| City |
shanghai |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE236720 |
Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [RNA-seq] |
| GSE236728 |
Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer |
|
| Relations |
| BioSample |
SAMN36344223 |
| SRA |
SRX20927763 |
