|
| Status |
Public on Dec 24, 2019 |
| Title |
RDtetCASZ1b_Ctrl-Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
RD cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Rhabdomyosarcoma
genotype: CASZ1b stably transfected RD cells (RDtetCASZ1b)
tetracycline status: untreated
|
| Treatment protocol |
RNA was isolated from RDtetCASZ1b cells that treated with or without Tet for 48 hr
|
| Growth protocol |
The CASZ1b stably transfected RD cells (RDtetCASZ1b) in which CASZ1b expression is tetracycline (Tet) inducible. The cells are cultured in RPMI 1640 containing 10% FBS.
|
| 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 HiSeq 2500 |
| |
|
| Description |
RNA-seq_RDtetCASZ1b_Tet_vs_Ctrl_CPM.txt
|
| 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
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample.
|
| |
|
| Submission date |
Feb 06, 2019 |
| Last update date |
Dec 24, 2019 |
| Contact name |
Jack Shern |
| Organization name |
NCI
|
| Lab |
POB
|
| Street address |
10 Center drive
|
| City |
bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE126146 |
RNA-sequencing analysis to investigate genes regulated by CASZ1 in RD cells |
| GSE126147 |
CASZ1 directly regulates expression of myogenic genes through regional epigenetic modifications to induce muscle and rhabdomyosarcoma cell differentiation |
|
| Relations |
| BioSample |
SAMN10880502 |
| SRA |
SRX5341908 |
