|
| Status |
Public on Jan 03, 2023 |
| Title |
Shep N-MYC-ER Replicate 2 MYC-ON CT44 |
| Sample type |
SRA |
| |
|
| Source name |
neuroblastoma cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: neuroblastoma cancer
cell line: Shep
cell type: neuroblastoma cancer cells
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 using the Qiagen RNeasy Plus kit according to manufacturer's instructions.
mRNA library with poly-A enrichment, second-strand synthesis, sequencing adaptor ligation, and PCR amplification. Libraries were sequences on an Illumina NovaSeq 6000 as 150PE (paired-end), yielding an average of 54.7 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 |
SHEP_Rep2_MYC-ON_44
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt
|
| Data processing |
Raw reads were processed by Novogene to demultiplex, remove reads containing adaptors, remove reads containing N > 10% (N represents the base cannot be determined), and remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
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-CG)
|
| |
|
| Submission date |
Dec 15, 2022 |
| Last update date |
Jan 03, 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) |
| GSE221103 |
Circadian time-series RNA-sequencing of SHEP and SKNAS neuroblastoma cells with inducible N-MYC-ER |
| GSE221174 |
MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis |
|
| Relations |
| BioSample |
SAMN32254116 |
| SRA |
SRX18716837 |
