|
| Status |
Public on Aug 01, 2014 |
| Title |
C2C12_GM_Ago2_CLIP-Seq_myoblast |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: myoblast
antibody: monoclonal anti-EIF2C2 antibody (M01)
antibody source: Abnova catalog number H00027161-M01
antibody lot number: 07344-S2
|
| Treatment protocol |
To induce C2C12 cell differentiation, cells were first grown to reach 80-90% confluency and the growth medium GM was subsequently replaced with the differentiation media DM (DMEM plus 2% horse serum) and continually cultured for 4 days.
|
| Growth protocol |
C2C12 myoblasts were maintained in Dulbecco’s minimal essential medium (DMEM; Life Technology) supplemented with 10% FBS (Life Technology).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
C2C12 Cells (GM or DM) were UV-irradiated at 400 mj and collected by scraping the cells from 15-cm plates. Ago2 immunoprecipitation was done in 1% NP-40 wash buffer.
3' adaptor was first added to the immunoprecipitated Ago2 complex on beads, then the eluted protein-RNA complex was subject to 10% Novex NUPAGE gel. After transfering to NC membrane, the corresponding band was cut and RNA was extracted. After 5' adaptor liagtion, RT-PCR was performed by using Super Script III and Ex taq polymerase.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
library from Ago2-RNA complex in C2C12 myoblasts
two replicates were combined to make one bedGraph file for the plus strand and one bedGraph file for the minus strand
|
| Data processing |
CLIP-seq: After removing 5' barcode (NNNT) and 3' adaptor sequence (CTCGTATGCCGTCT), the tags longer than 20 nt were mapped to the reference mouse genome (mm10) with Bowtie2 (version 2.0.0-beta7 with parameters --very-sensitive -rdg 5,2 --score-min L, -0.6, -0.7)
Genome_build: mm10
|
| |
|
| Submission date |
May 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bo Yang |
| E-mail(s) |
yangbobio@gmail.com
|
| Organization name |
College of Life Sciences, Wuhan University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
6101
|
| Street address |
Luo-jia-shan, Wuchang
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE57596 |
MicroRNA Directly Enhances Mitochondrial Translation during Muscle Differentiation. |
|
| Relations |
| BioSample |
SAMN02770264 |
| SRA |
SRX540938 |
