|
| Status |
Public on Nov 18, 2022 |
| Title |
Control siRNA 16h-1 |
| Sample type |
SRA |
| |
|
| Source name |
human myoblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Myoblast
sirna: Control siRNA 16h
|
| Treatment protocol |
Final concentration of 50 nM siRNA and Lipofectamine RNAiMAX (Thermo Fisher Scientific) of control small interfering RNA (Ctrl siRNA) or LncFAM siRNA was transfected 24 h before induction of differentiation.
|
| 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 |
Control siRNA replicate-1 16h
|
| 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: geneCOUNT.txt: Tab-delimited text files containing counts.
|
| |
|
| Submission date |
May 26, 2022 |
| Last update date |
Nov 18, 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) |
| GSE204886 |
Enhanced myogenesis through LncFAM-mediated recruitment of HNRNPL to the MYBPC2 promoter I |
| GSE215343 |
Enhanced myogenesis through LncFAM-mediated recruitment of HNRNPL to the MYBPC2 promoter |
|
| Relations |
| BioSample |
SAMN28680558 |
| SRA |
SRX15470566 |
