|
| Status |
Public on Jul 18, 2023 |
| Title |
SKNAS N-MYC-ER MYC-ON CT64 Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
neuroblastoma cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: neuroblastoma cancer
cell line: SKNAS
cell type: neuroblastoma cancer
genotype: N-MYC-ER overexpressing
treatment: 4OHT (MYC-ON), dexamethasone
|
| Growth protocol |
Cells were cultured in DMEM high glucose with 10% fetal bovine serum in a 5% CO2 incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the Omega Bio-Tek E.Z.N.A.® HP Total RNA Kit according to manufacturer's instructions.
mRNA library preparation with the Illumina TruSeq Stranded mRNA kit . Libraries were sequenced on an Illumina NovaSeq 6000 as 100PE (paired-end), yielding an average of 93.1 million reads per sample (when adding together both paired ends).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ON_64
|
| Data processing |
Raw reads were processed by the GRC to demultiplex, then with FASTP to trim adaptors and remove reads that were low quality or too short.
Processed reads were mapped to transcripts using Salmon 1.3.0 in mapping-based mode for paired-end samples, using a decoy-aware transcriptome built from Gencode v35 GRCh38 primary assembly genome and v35 transcriptome. Salmon further filtered out ambiguous reads or reads that corresponded to decoy fragments.
Transcripts were collapsed to gene-level using Tximport 1.12.3 using Gencode v35 transcriptome. Genes were annotated with symbols using the Ensembl GRCh38.101 transcriptome annotations.
Tximport normalized raw counts to Transcripts-Per-Million (TPM).
Assembly: hg38
Supplementary files format and content: Tab-delimited text with GENEID (Column A), SYMBOL (Column B) and TPM data of samples (Columns C-AB)
|
| |
|
| Submission date |
Jul 18, 2023 |
| Last update date |
Jul 18, 2023 |
| Contact name |
Brian James Altman |
| E-mail(s) |
brian_altman@urmc.rochester.edu
|
| Phone |
5852765877
|
| Organization name |
University of Rochester
|
| Department |
Biomedical Genetics
|
| Street address |
601 Elmwood Avenue Box 633
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14620 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE221174 |
MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis |
| GSE237608 |
Circadian time-series RNA-sequencing of SKNAS neuroblastoma cells with inducible N-MYC-ER, Replicate #2 |
|
| Relations |
| BioSample |
SAMN36511065 |
| SRA |
SRX21060520 |
