|
| Status |
Public on Oct 19, 2023 |
| Title |
IMR32_siMYCN_48h_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
IMR32 Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR32
cell type: Neuroblastoma
treatment: siMYCN
|
| Treatment protocol |
siRNAs were transiently transfected into IMR32 cells using Nucleofector electroporation (Lonza) and cultured in growth medium for 48 hr before RNA extraction.
|
| Growth protocol |
IMR32 cells are maintained in growth medium. Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen Rneasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample_35_siMYCN48hIMR_r3
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using STAR 2.5.1
Counts per million (CPM) were quantified using the Partek E/M model
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include CPM values for each Sample.
|
| |
|
| Submission date |
Jul 18, 2022 |
| Last update date |
Oct 19, 2023 |
| Contact name |
Zhihui Liu |
| E-mail(s) |
[email protected]
|
| Phone |
2408583857
|
| Organization name |
National Cancer Institute
|
| Street address |
9000 rockville pike
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE208420 |
RNA-sequencing analysis to identify genes regulated by MYCN, WDR5 and G9a in neuroblastoma cell line IMR32 |
| GSE208424 |
The cooperation between MYCN and its cofactors WDR5 and G9a |
|
| Relations |
| BioSample |
SAMN29802227 |
| SRA |
SRX16322600 |
