|
| Status |
Public on Jun 13, 2022 |
| Title |
AB678 Ctrl TSB 48h-2 |
| Sample type |
SRA |
| |
|
| Source name |
human myoblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AB678
cell type: Human myoblast
cell status: Differentiated for 48h
treatment: transfected Ctrl TSB for 24h
|
| Treatment protocol |
Human myoblasts were transfected with 50 nM TSB to block the interaction between OIP5-AS1 and miR-7 or with scrambled controls; 24 h later, the cells were replaced to frash growth medoium for 24h or induced to differentiate by replacement of the growth medium with differentiation medium for the indicated time points.
|
| Growth protocol |
Human myoblasts were cultured in growth medium (equal volume mixture of Hamm's F10 media with 20% FBS and Promocell Skeletal Muscle Cell Growth Medium). Human myoblasts were induced to differentiate by growth to high density and replacement of the growth medium with differentiation medium (DMEM with 2% horse serum)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cultured cells was isolated using the Direct-zol™ RNA MiniPrep kit (Zymo Research), which includes a digestion step using DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
transfected Ctrl TSB for 24h and further transfered into differentiated medium for 48h human myoblast replicate-2
|
| Data processing |
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Assembly: hg19
Supplementary files format and content: text files containing counts
|
| |
|
| Submission date |
May 11, 2022 |
| Last update date |
Jun 14, 2022 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE202752 |
LncRNA OIP5-AS1-directed miR-7 degradation promotes MYMX production during human myogenesis |
| GSE202793 |
LncRNA OIP5-AS1-directed miR-7 degradation promotes MYMX production during human myogenesis |
|
| Relations |
| BioSample |
SAMN28192752 |
| SRA |
SRX15233797 |
