|
Status |
Public on Dec 24, 2019 |
Title |
CTRtetEV_Dox-Rep1 |
Sample type |
SRA |
|
|
Source name |
SMS-CTR cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: Rhabdomyosarcoma cell line: SMS-CTR genotype: CTRtetEV dox treatment status: Dox-treated
|
Treatment protocol |
RNA was isolated from CTRtetCASZ1b cells that treated with or without Dox for 48 hr
|
Growth protocol |
The CASZ1b stably transfected SMS-CTR cells (CTRtetCASZ1b) are cultured in RPMI 1640 containing 10% FBS. CASZ1b expression is induced by Dox treatment.
|
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 4000 |
|
|
Description |
RNA-seq_CTRtetCASZ1b-CTRtetEV_Dox_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 |
GPL20301 |
Series (2) |
GSE126145 |
RNA-sequencing analysis to investigate genes regulated by CASZ1 in SMS-CTR cells |
GSE126147 |
CASZ1 directly regulates expression of myogenic genes through regional epigenetic modifications to induce muscle and rhabdomyosarcoma cell differentiation |
|
Relations |
BioSample |
SAMN10880494 |
SRA |
SRX5341916 |