|
| Status |
Public on Aug 30, 2023 |
| Title |
JR1 cells, shSCR |
| Sample type |
SRA |
| |
|
| Source name |
JR1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: JR1
cell type: Fusion-Negative Rhabdomyosarcoma
genotype: WT
|
| Growth protocol |
RD, JR1 cells were cultured in DMEM high-glucose (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% penicillin-streptomycin. All the cell lines were cultured at 37°C in a humidified atmosphere of 5% CO2/ 95% air and regularly checked for mycoplasma contamination.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from JR1 and RD FN-RMS cell lines, using the RNeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit following manifacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence reads were aligned to the GRCh38 reference genome usign STAR v2.7.9a.
Gene expression was calculated as Trasnscript Per Million (TPM) reads using RSEM V1.3.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
|
| |
|
| Submission date |
Aug 21, 2023 |
| Last update date |
Aug 30, 2023 |
| Contact name |
Matteo Cassandri |
| E-mail(s) |
matteo.cassandri@gmail.com
|
| Organization name |
Bambino Gesù Children's Hospital
|
| Department |
Department of Oncohematology
|
| Street address |
Viale di San Paolo 15
|
| City |
Rome |
| ZIP/Postal code |
00146 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE241282 |
A MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57Kip2 targeting [RNA-seq] |
| GSE241283 |
A MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57Kip2 targeting |
|
| Relations |
| BioSample |
SAMN37105279 |
| SRA |
SRX21446325 |
