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Sample GSM4274788 Query DataSets for GSM4274788
Status Public on Jan 16, 2023
Title Mice NFA Rep 3
Sample type SRA
 
Source name freshly isolated mice muscle stem cells
Organism Mus musculus
Characteristics cell type: muscle stem cells
treatment: NFA
Treatment protocol Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 (GIBCO), 20% horse serum (Atlanta Biologics), 1% penicillin-streptomycin (Invitrogen), 1% GlutaMAX (Invitrogen), and 5 ng/ml bFGF (Sigma) at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C, respectively.
Growth protocol Freshly isolated mice muscle stem cells were sorted into collagen/laminin-coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells, which were cultured in a zESC medium composed of 70% LDF medium (50% Leibowitz’s L-15 (Invitrogen), 35% DMEM (Invitrogen), and 15% Ham’s F-12 (Invitrogen)), with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein (Sigma-Aldrich), 15 mM sodium bicarbonate, 15 mM HEPES (Invitrogen),1% L-glutamine (Invitrogen), 10 nM sodium selenite (Sigma-Aldrich), 1% N2 (Invitrogen), 2% B27 (Invitrogen), 0.1 mg/ml Primocin (Invivogen) and at 28°C without CO2 for 48 hours.
Extracted molecule total RNA
Extraction protocol Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS, then total RNA was extracted with the micro RNeasy kit (QIAGEN).
cDNA was prepared using SMART Seq v4 Ultra Low RNA-Seq kit (Takara) and a Nextera kit was used for library construction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description NFAplus3
Data processing Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: GRCz11 and GRCm38
Supplementary_files_format_and_content: FPKM
 
Submission date Jan 16, 2020
Last update date Jan 16, 2023
Contact name Leonard Zon
E-mail(s) zon@enders.tch.harvard.edu
Organization name Boston Children's Hospital
Department Oncology/Hematology
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL19057
Series (1)
GSE143801 Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species
Relations
BioSample SAMN13872809
SRA SRX7571702

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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