|
| Status |
Public on Jun 21, 2010 |
| Title |
C2C12 with actinomycin D, time 10 min, rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
C2C12 with actinomycin D, time 10 min
|
| Organism |
Mus musculus |
| Characteristics |
cell line: CRL-1772 (ATCC)
cell type: proliferating C2C12 (LKO-1) cells (<70% confluency)
|
| Treatment protocol |
Transcription was inhibited by addition of Actinomycin-D (8μg/mL Sigma) for a period of 30 min.
|
| Growth protocol |
C2C12 cells were obtained from ATCC (CRL-1772). These cell lines were cultured in DMEM with 10% FBS, 10 U/ml penicillin, 10 µg/ml streptomycin, and 1g/ml puromycin. The cells were maintained below 70% confluency to prevent differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected in Trizol™ (Invitrogen) at the indicated time points following the incubation and total RNA was prepared according to the manufacturers instructions. RNA concentration, purity, and quality were determined via Bioanalyzer (Agilent).
|
| Label |
biotin
|
| Label protocol |
Biotinylated DNA probes were prepared according to Whole Transcript Sense Target Labeling Manual (Affymetrix)
|
| |
|
| Hybridization protocol |
300ng of total RNA for half life arrays were used to generate labeled cDNA fragments for hybridization to Mouse Affymetrix Gene 1.0 ST Arrays following the manufacturer’s protocol (GeneChipTM WT cDNA Synthesis Kit #900652 and #900720).
|
| Scan protocol |
GeneChips were scanned using Affymetrix GeneChip 3000G
|
| Description |
This sample was collected at 10 min after actinomycin D treatment
|
| Data processing |
Transcripts whose probe sets with detection above background (DABG) P-value < 0.05 in at least 2 out of 3 replicates at the 0 min time point were considered expressed and used for subsequent analyses. All probe set values were normalized to the 5th percentile value of all probe sets on the same array.
|
| |
|
| Submission date |
Apr 07, 2010 |
| Last update date |
Jun 16, 2010 |
| Contact name |
Ju Youn Lee |
| Organization name |
UMDNJ-New Jersey Medical School
|
| Department |
Biochemistry
|
| Street address |
185 South Orange Ave. MSB-E501
|
| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07101 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (3) |
| GSE21233 |
Expression data from C2C12 mouse myoblast with treatment actinomycin D |
| GSE21236 |
Systematic analysis of cis-elements in unstable mRNAs demonstrates that CUGBP1 is a key regulator of mRNA decay in muscle cells |
| GSE35944 |
The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts |
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