|
| Status |
Public on Apr 27, 2021 |
| Title |
KO_Polysome_associated_Bio_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
developmental stage: GM 48 hours
genotype: Dhx36 KO
|
| Treatment protocol |
C2C12 myoblasts were treated by 100 μg/ml of cycloheximide in culture medium and incubated at 37℃ for 10 min.
|
| Growth protocol |
C2C12 myoblasts were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total cytoplasmic RNA or RNA bound by more than 4 ribosomes were extracted using TRIzol LS reagent (Invitogen) following the manufacturer's instructions and then subjected to poly(A) selection by using mRNA purification beads (Ambion, 61006).
RNA libraries were prepared by using NEBNext® Ultra™ II RNA Library Preparation Kit (NEB, E7770S) and barcoded libraries were pooled at equal concentration and sequenced on the HiSeq1500 platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Polysome-associated RNA
|
| Data processing |
Library strategy: Polysome profiling
Adaptor sequence trimming, quality filtering (i.e. quality<38 and length<22) and duplication removal were first conducted.
Remaining reads were aligned to the mouse genome mm9 using Tophat2 (v2.0.13) software with the following parameters: --no-coverage-search; --mate-std-dev 60.
Expression levels were quantified using Cufflinks with default parameters and annotated gene model (refGene for mm9) from UCSC.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.fpkm_tracking: Tab-delimited files from Cufflinks containing FPKM values.
|
| |
|
| Submission date |
May 24, 2020 |
| Last update date |
Apr 27, 2021 |
| Contact name |
Jie Yuan |
| E-mail(s) |
jieyuan@link.cuhk.edu.hk
|
| Organization name |
The Chinese University of Hong Kong
|
| Department |
Orthopaedics and Traumatology
|
| Lab |
Wang Lab
|
| Street address |
Prince of Wales Hospital
|
| City |
HONG KONG |
| State/province |
HONG KONG |
| ZIP/Postal code |
NA |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE151123 |
System-wide analysis of Dhx36 function in skeletal muscle satellite cells reveals its binding with 5’UTR G4 structure to promote Gnai2 RNA translation [Polysome profiling] |
| GSE151124 |
System-wide analysis of Dhx36 function in skeletal muscle satellite cells reveals its binding with 5’UTR G4 structure to promote Gnai2 RNA translation |
|
| Relations |
| BioSample |
SAMN15009204 |
| SRA |
SRX8389145 |
