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Sample GSM4567045 Query DataSets for GSM4567045
Status Public on Apr 27, 2021
Title WT_Polysome_associated_Bio_Rep1
Sample type SRA
 
Source name C2C12 myoblasts
Organism Mus musculus
Characteristics cell line: C2C12
developmental stage: GM 48 hours
genotype: Wild Type
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 SAMN15009207
SRA SRX8389142

Supplementary file Size Download File type/resource
GSM4567045_WT_Poly_Rep1.genes.fpkm_tracking.gz 672.2 Kb (ftp)(http) FPKM_TRACKING
GSM4567045_WT_Poly_Rep1.isoforms.fpkm_tracking.gz 1.0 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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