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Sample GSM5625095 Query DataSets for GSM5625095
Status Public on Oct 15, 2021
Title K001-3D-1
Sample type SRA
 
Source name Bone marrow
Organism Homo sapiens
Characteristics cell type: Mesenchymal Stem Cell
treatment: 3D
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 SAMN22251008
SRA SRX12597577

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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