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Sample GSM7797304 Query DataSets for GSM7797304
Status Public on Sep 22, 2023
Title Fetal_W20_Tissue. Myofiber_rep7
Sample type SRA
Source name 008
Organism Homo sapiens
Characteristics slide name: NCB_PosCntl2
segment label: MyoFiber
cell type: Fetal Tissue
treatment: None
pax7+: False
pax7-laminac+: False
engraft fetal actc1+: False
engraft fetal actc1-: False
hpsc myofiber: False
tissue myofiber: True
label microscope_slide: NCB_PosCtrl2
Treatment protocol Experiment 2-3. Mice were intramuscularly injected with 50µL of 1.2% BaCl2 into the tibilias anterior to induce injury. Endogenous mouse Pax7+ cells were ablated prior to transplantation with 400mg/kg tamoxifen chow for 7 days prior to being fed normal chow during experiments. Experiment 3 only. Mice were injected intraperitoneally with AP1903 (10μM in 100μl saline) or control (0.1% DMSO in saline) every two weeks for 90 days (six total injections).
Growth protocol hPSCs were cultured in mTESR media, while hPSC derived SMPCs were cultured in SKGM2 media.
Extracted molecule total RNA
Extraction protocol Mice tibialis anterior skeletal muscle was flash frozen and sectioned at 10µm onto glass coverslips
Following overnigh hybridization, same day primary and secondary antibody stain: Cyto13 (488), ACTC1 (Rb IgG-555), Lamin AC and Spectrin (Ms IgG2b 594), PAX7 (Ms IgG1-647)
Manufacturer protocol was followed except with modifications: 0.025 µg/mL Proteinase K for 5 minutes . No antigen retrieval. No 65C baking step. Primary and secondy antibody staining performed
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description (v1.0) Human NGS Whole Transcriptome Atlas RNA
GeoMx readout mode: NGS
Data processing Matrix 1: This is a matrix of Deseq2 counts for hPSC SMPC control, fetal SMPC transplant, fetal tissue, and adult tissue. GeoMx platform analysis was conducted with a 5% target filter, including all flagged ROIs. This input was Q3 normalized before exporting the dataset and uploading into R Studio for Deseq2 analysis to obtain PCA plots.
Matrix 2: This is a matrix of Q3 normalized counts for control and AP1903 treated hPSC SMPC . GeoMx platform analysis was conducted with a 20% target filter, including all flagged ROIs. Then, Q3 normalization was conducted.
Matrix shows total normalized counts of RNA oligos.
Submission date Sep 22, 2023
Last update date Sep 23, 2023
Contact name Michael Hicks
Phone 7606175095
Organization name University of California, Irvine
Street address 845 Health Sciences Road, Room 3101
City Irvine
State/province CA
ZIP/Postal code 92617
Country USA
Platform ID GPL18573
Series (1)
GSE243875 Spatial RNA sequencing analysis confirm ACTC1+ myofibers support a transplanted SMPC pool
BioSample SAMN37518980
SRA SRX21865193

Supplementary file Size Download File type/resource
GSM7797304_DSP-1001660009146-A-B04.dcc.gz 57.5 Kb (ftp)(http) DCC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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