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Sample GSM8381328 Query DataSets for GSM8381328
Status Public on Dec 23, 2024
Title GFP_MEF2C2
Sample type SRA
 
Source name skeletal muscle
Organism Mus musculus
Characteristics tissue: skeletal muscle
genotype: KO
treatment: MEF2C-GFP
Extracted molecule polyA RNA
Extraction protocol total RNA was extracted from frozen tissues and checked for quality and quantity by nanodrop and 2100/GX
1ug total RNA was prepared for cDNA libraries using cDNA-PCR Sequencing Kit (SQK-LSK110+EXP-PCB096) protocol provided by Oxford Nanopore Technologies(ONT). Briefly,the template switching activity of reverse transcriptases enrich for full-length cDNAs and add defined PCR adapters directly to both ends of the first-strand cDNA. And following cDNA PCR for 14 circles with LongAmp Tag (NEB). The PCR products were then subjected to ONT adaptor ligation using T4 DNA ligase (NEB). Agencourt XP beads was used for DNA purification according to ONT protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model PromethION
 
Data processing Raw reads were first filtered with minimum average read quality score=6 and minimum read length=350bp. Ribosomal RNA were discarded after mapping to rRNA database. Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads. Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish.
Consensus sequences were mapped to reference genome using minimap2. Mapped reads were further collapsed by cDNA_Cupcake package with min-coverage=85% and min-identity=90%. 5’ difference was not considered when collapsing redundant transcripts.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with a Pvalue < 0.05 and foldchange ≥ 1.5 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm38_release95
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes CPM for each Sample
 
Submission date Jul 07, 2024
Last update date Dec 23, 2024
Contact name Mei Yang
E-mail(s) yangmei23@csu.edu.cn
Phone (86)13548641787
Organization name The Second Xiangya Hospital, Central South University
Street address 139 Middle Renmin Road
City Changsha
ZIP/Postal code 410011
Country China
 
Platform ID GPL26624
Series (2)
GSE243334 PRR14 mediates mechanotransduction and regulates myofiber identity via MEF2C in skeletal muscle
GSE271657 PRR14 mediates mechanotransduction and regulates myofiber identity via MEF2C in skeletal muscle
Relations
BioSample SAMN42353675
SRA SRX25230286

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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