|
Status |
Public on Oct 15, 2021 |
Title |
K001-2D-1 |
Sample type |
SRA |
|
|
Source name |
Bone marrow
|
Organism |
Homo sapiens |
Characteristics |
cell type: Mesenchymal Stem Cell treatment: 2D source: Bone marrow derived
|
Treatment protocol |
Each triplicate of cell group was cultured under 2D or 3D culture conditions.
|
Growth protocol |
hMSCs were expanded and maintained in complete culture media (CCM) containing α-MEM with 10% fetal bovine serum and 1% Penicillin/Streptomycin in a standard incubator at 37°C with 5% CO2 and 20% O2. For 2D culture, hMSCs were seeded at a density of 1500 cells/cm2. For 3D culture, hMSCs at passage 4 to 7 were suspended in CCM and 1.0×105 hMSCs in 2.0 mL CCM were seeded in each well of ultra-low attachment (ULA) 6-well plates. The ULA plates were then placed on a rocking base of a WAVE Bioreactor in a standard humidified incubator (37°C, 5% CO2) under controlled rocking angles (i.e., 8°) and rocking speeds (i.e., 20 rockings/min, or rpm) for 48 hours.
|
Extracted molecule |
total RNA |
Extraction protocol |
Cell total RNA was isolated with Trizol under manufacturer's protocol. Isolated RNA was incubated with DNase I to remove trace genomic DNA contamination. Then, mRNA library was prepared by combination of NEBNext Ultra RNA Library Prep Kit (NEB, E7530) and NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). The library ran on Bioanalyzer with HS DNA chip (Agilent; 5067-4626) for quality control and quantified by KAPA library qPCR kit (KAPA; KR0405).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
Donor K001
|
Data processing |
RAW data were uploaded to BaseSpace (Illumina) for quality control and base calling. Qulified reads were aligned to the hg38 human reference genome. Data was uploaded to NetworkAnalyst 3.0 for further analysis and network visualization. Total counts were filtered by following specifications: counts less than 10, variance less than 10% and unannotated, and then normalized by Log2-counts per million. Genome_build: hg38 Supplementary_files_format_and_content: Process counts file (xlsx) was generated and normalized by NetworkAnalyst.
|
|
|
Submission date |
Oct 13, 2021 |
Last update date |
Dec 20, 2021 |
Contact name |
li sun |
E-mail(s) |
lsun2@fsu.edu, davidgmeckes@gmail.com
|
Organization name |
Florida State University
|
Department |
College of medicine
|
Street address |
1115 west call st.
|
City |
Tallahassee |
State/province |
FL |
ZIP/Postal code |
32306 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE185874 |
Engineering Extracellular Vesicles by Three-dimensional Dynamic Culture of Human Mesenchymal Stem Cells |
|
Relations |
BioSample |
SAMN22251010 |
SRA |
SRX12597575 |