|
| Status |
Public on Nov 18, 2022 |
| Title |
Control_48h |
| Sample type |
SRA |
| |
|
| Source name |
human myoblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human myoblast
cell status: 48 hrs differentiation
|
| Treatment protocol |
AB678 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) for 48 hours.
|
| 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 |
200 ng Total RNA was extracted from AB678 48 hours into differentiation
RNA libraries were prepared for sequencing using the Nanopore cDNA-PCR sequencing kit (SQK-PCS111) as per the manufacturer's intsructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Description |
Control_48h
|
| Data processing |
FAST5 files were converted to standard FASTQ files using the Guppy program ( 6.0.1+652ffd1).
FASTQ files were aligned to human genome hg19 Ensembl v82 using Minimap2 software v2.17-r941.
Stringtie2 (v2.2.1) was used to assemble isoforms.
SQANTI3 (v4.3) was used for isoform identification and quality control.
Assembly: hg19
Supplementary files format and content: GTF file containing assembled isoforms
|
| |
|
| Submission date |
Oct 12, 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 |
GPL26167 |
| Series (2) |
| GSE215327 |
Enhanced myogenesis through LncFAM-mediated recruitment of HNRNPL to the MYBPC2 promoter II |
| GSE215343 |
Enhanced myogenesis through LncFAM-mediated recruitment of HNRNPL to the MYBPC2 promoter |
|
| Relations |
| BioSample |
SAMN31253738 |
| SRA |
SRX17864492 |
