|
| Status |
Public on Dec 08, 2020 |
| Title |
LncMyoD-KO clone 2 no treatment Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H
cell type: fibroblast
genotype: LncMyoD-KO
treatment: no treatment
|
| Treatment protocol |
Cells were treated with MyoD adenovirus or LncMyoD-containing plasmid to induce transdifferentiation.
|
| Growth protocol |
10T1/2 fibroblasts were cultured in DMEM supplemented with 10%FBS and changed to DMEM supplmented with 2%HS after MyoD-induced transdifferentiation.
|
| 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 cDNA was then tagmented using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and amplified to construct RNA-seq library . The libraries were sequenced using DNBSEQ-G400 sequencer (BGI) (2 x 100)).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
no treatment
|
| 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 |
Oct 06, 2020 |
| Last update date |
Dec 09, 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 |
GPL28457 |
| Series (1) |
| GSE159133 |
Transcriptome sequencing analysis of MyoD-induced transdifferentiation in 10T1/2 fibroblasts using RNA-seq |
|
| Relations |
| BioSample |
SAMN16382373 |
| SRA |
SRX9251449 |
