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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jan 16, 2023 |
Title |
Mice DMSO Rep 2 |
Sample type |
SRA |
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Source name |
freshly isolated mice muscle stem cells
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Organism |
Mus musculus |
Characteristics |
cell type: muscle stem cells treatment: DMSO
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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.
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
DMSOplus
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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
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Submission date |
Jan 16, 2020 |
Last update date |
Jan 16, 2023 |
Contact name |
Leonard Zon |
E-mail(s) |
zon@enders.tch.harvard.edu
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Organization name |
Boston Children's Hospital
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Department |
Oncology/Hematology
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Street address |
1 Blackfan Circle
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (1) |
GSE143801 |
Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species |
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Relations |
BioSample |
SAMN13872807 |
SRA |
SRX7571704 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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