|
| Status |
Public on Oct 16, 2019 |
| Title |
Myoblast shCTRL rep1 |
| Sample type |
SRA |
| |
|
| Source name |
human myoblasts
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: shCTRL
cell type: myoblasts
|
| Treatment protocol |
Cells were harvested following acutase treatment and processed for total RNA extraction
|
| Growth protocol |
Human iPSC-derived neural progenitors were obtained from Stem Cell Technologies (cat# 70901) and culture in neural progenitor medium 2 (Stem Cell Technologies, cat# 08560). Differentiation into neurons was achieved using the STEMdiff™ Neuron Differentiation Kit (Stem Cell Technologies, cat# 08500). Primary human skeletal myoblasts were obtained from Thermo Fisher (Gibco, A12555) and cultured in MegaCell DMEM (Sigma) containing 5% FBS (Lonza), 2 mM glutamine (Life Technologies), 0.1mM β-mercaptoethanol (Life Technologies), 1X MEM Non-Essential Amino Acids Solution (Life Technologies), 5 ng/ml bFGF (Peprotech), Penicillin (100 U/mL), Streptomycin (100 μg/mL).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed using the miRNeasy mini kit (Qiagen). RNA was eluted from the columns using RNase-free water and quantified using a Nanodrop ND-1000.
RNA sequencing libraries were prepared using the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#: E7420). The RNA input for library construction was 50 ng total. Libraries were amplified for 14 cycles. Post library constructions, the samples were validated using 2200 Tapestation System and High Sensitivity D1000 ScreenTape kit. Libraries were quantified using the Kapa Biosystems Library Quantification kit (Catalog Number KK4828) and the BioRad CFX96 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
hMyoblasts shCTRL
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Genome_build: Homo sapiens UCSC hg19
|
| |
|
| Submission date |
Dec 18, 2018 |
| Last update date |
Oct 16, 2019 |
| Contact name |
Fei Ji |
| Organization name |
Massachusetts General Hospital
|
| Street address |
185 Cambridge St
|
| City |
Boston |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE112479 |
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells |
| GSE124072 |
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN10612669 |
| SRA |
SRX5162006 |
