|
| Status |
Public on Dec 24, 2019 |
| Title |
C2C12_CASZ1b-Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Undifferentiated C2C12
transfected with: CASZ1b
|
| Treatment protocol |
CASZ1a, CASZ1b or EV was transiently transfected into C2C12 cells by nucleofector electroporation and cultured in GM for 48 hr before RNA extraction. To generate Casz1 stable knockdown, C2C12 cells were infected with control shRNA (shCtrl) or Casz1 shRNA (shCasz1) particles. The stable Casz1 knockdown cells were cultured in DM for 48 hr before RNA extraction.
|
| Growth protocol |
C2C12 cells are maintained in growth medium. To induce C2C12 cells differentiation, the cells are cultured in differentiation medium. Growth medium: DMEM, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine. Differentiation medium: DMEM, 2% horse 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 HiSeq 4000 |
| |
|
| Description |
RNA-seq_C2C12_CASZ1_Overexpression_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: mm10
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 |
GPL21103 |
| Series (2) |
| GSE126144 |
RNA-sequencing analysis to investigate genes regulated by CASZ1 in C2C12 cells |
| GSE126147 |
CASZ1 directly regulates expression of myogenic genes through regional epigenetic modifications to induce muscle and rhabdomyosarcoma cell differentiation |
|
| Relations |
| BioSample |
SAMN10880506 |
| SRA |
SRX5341931 |
