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Sample GSM3592301 Query DataSets for GSM3592301
Status Public on Dec 24, 2019
Title C2C12_shCasz1-Rep3
Sample type SRA
 
Source name C2C12 cells
Organism Mus musculus
Characteristics cell type: Differentiated C2C12
transfected with: shCasz1
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_shCasz1_vs_shCtrl_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 SAMN10880516
SRA SRX5341938

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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