|
| Status |
Public on Dec 08, 2020 |
| Title |
LncMyoD Knockdown Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Skeletal muscle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Muscle stem cells
treatment: LncMyod-knockdown
|
| Treatment protocol |
Cultured satellite cells were treated with siRNA targeting LncMyod for 48h before harvest
|
| Growth protocol |
Satellite cells were isolated from mouse hindlimb and cultured in F10 supplemented with 10% HS and P/S
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Medium was removed, and total RNA was isolated using NucleoSpin RNA XS (Macherey-Nagel).
cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol. The RNA-Seq libraries were sheared with a Covaris S220 and generated using Ovation Ultralow DR Multiplex System 9-16 (NuGEN Technologies). The libraries were sequenced using Illumina NextSeq 500 (2 x 150).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
cultured satellite cells treated with siRNA targeting LncMyod
|
| Data processing |
Illumina bcl2fastq v2.19 with default parameters was used for basecalling to generate demultiplexed FASTQ files.
To improve mappability of reads, low quality bases were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘SLIDINGWINDOW:10:20 MINLEN:30’.
Trimmed reads were mapped to mm10 using HISAT2 v2.1.0 (Kim et al., 2015) with default parameters. Unmapped reads and read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 516 -q 10 -b’.
After read mapping, StringTie v1.3.3 (Pertea et al., 2015) was used with the default parameters and the Gencode vM19 gene annotation GTF file to estimate the expression of annotated transcripts.
Ballgown v2.2.0 (Frazee et al., 2015) was used to calculate gene expression FPKM values and output the gene expression table.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated value table of genes with their corresponding FPKM values as output by Ballgown
|
| |
|
| Submission date |
Apr 12, 2019 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Tom Cheung |
| Organization name |
Hong Kong University of Science and Technology
|
| Department |
Division of Life Science
|
| Street address |
Clear Water Bay, Kowloon
|
| City |
Hong Kong |
| ZIP/Postal code |
N/A |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE129766 |
Transcriptome sequencing analysis of LncMyod-knockdown satellite cells by RNA-seq |
| GSE129768 |
A Long Noncoding RNA, LncMyod, Regulates Myogenic Lineage Progression by Modulating Chromatin Accessibility |
|
| Relations |
| BioSample |
SAMN11411461 |
| SRA |
SRX5678396 |
