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Sample GSM6744009 Query DataSets for GSM6744009
Status Public on Sep 22, 2023
Title Deficient 4
Sample type RNA
 
Source name Subcutaneous myocardial matrix hydrogel injection and nearby dorsal skin
Organism Mus musculus
Characteristics Sex: male
strain: w-sh mice: B6.Cg-KitW-sh/HNihrJaeBsmJ
age: 12-14 weeks old
Treatment protocol Mice received 2x subcutaneous injections in the dorsal region of porcine-derived decellularized myocardial matrix hydrogels.
Growth protocol Male mast cell deficient mice (w-sh mice: B6.Cg-KitW-sh/HNihrJaeBsmJ, Jackson Laboratory, Sacramento, CA), mast cell engrafted mice and wild-type C57BL6/J were housed till 11-13 week old before performing procedures. Hydrogels were isolated at 11 days post-injection based on latest timepoint for discernible presence hydrogel degradation profile and analyzed for gene expression analysis by Nanostring Mouse Immunology Panel. Mast cell-engrafted mice were created by delivering eight to ten 100 µL subcutaneous injections of bone marrow differentiated mast cells in DMEM totaling 4 million cells. Injections were at evenly spaced intervals throughout the dorsal region of 4-6 week old deficient mice.
Extracted molecule total RNA
Extraction protocol 11 days post-injection, mice were euthanized by sodium
Label Codeset barcode consisting of 4 fluorophores for identifying each specific hybridized gene probe.
Label protocol 100 ng of total RNA per sample were labeled with Immunology Panel Reporter CodeSet solution along with relevant buffers and master mix based on manufacturer instructions.
 
Hybridization protocol Capture ProbeSet was added to each vessel, mixed and placed on a thermocycler at 65ºC for 16-48 hours before being maintained at 4ºC for less than 24 hours. Nanostring nCounter Prep Station performed automated fluidic sample processing to purify and immobilize hybridized sample to cartridge surface.
Scan protocol Immobilized digitial barcode reads from probes hybridized with RNA sample were read on cartridge surface with the Nanostring nCounter Digital Analyzer.
Description Samples were processed according to manufacturer instructions. In brief, RNA sample concentrations were measured on a Qubit 3.0 Fluorometer with a QubitTM RNA HS Assay kit. 70 µL of hybridization buffer was mixed with Immunology Panel Reporter CodeSet solution, and 8 µL of this master mix was mixed in a separate reaction vessel with 100 ng of RNA per tissue sample and RNA-free water up to 13 µL total. 2 µL of Capture ProbeSet was added to each vessel, mixed and placed on a thermocycler at 65ºC for 16-48 hours before being maintained at 4ºC for less than 24 hours. Nanostring nCounter Prep Station performed automated fluidic sample processing to purify and immobilize hybridized sample to cartridge surface. Digital barcode reads were analyzed by Nanostring nCounter® Digital Analyzer.
kg2
Data processing Data was exported through the manufacturer nSolverTM Analysis Software 4.0 and analyzed through custom R scripts under R versions 4.04 with normalized counts determined by the NanostringDiff package and thresholding outside of one standard deivation from the mean signal from the negative control probes. Specific scripts uploaded to Wang, Raymond M. (2022). NanoString Differential Expression Analysis with NanoStringDiff package (Version 6). Zenodo. 10.5281/zenodo.7190262
 
Submission date Nov 19, 2022
Last update date Sep 22, 2023
Contact name Raymond Ma Wang
E-mail(s) ruimawang@gmail.com
Organization name University of California San Diego
Department Bioengineering
Lab Sanford Consortium for Regenerative Medicine
Street address 2880 Torrey Pines Scenic Dr
City La Jolla
State/province California
ZIP/Postal code 92037
Country USA
 
Platform ID GPL30438
Series (1)
GSE218383 Nanostring gene expression data, comparison of response to subcutaneously implanted porcine-derived decellularized myocardial matrix hydrogels in mast cell deficient mice compared to deficient mice with mast cell engraftment and wild-type C57BL6/J mice

Data table header descriptions
ID_REF
VALUE Normalized signal intensity with genes thresholded based on one standard deviation from the negative control probe signal mean value.

Data table
ID_REF VALUE
Abcb10 250.306235122144
Abcb1a 55.6236078049209
Abcf1 999.238383066972
Abl1 385.392139791238
Adal 177.465796329986
Ahr 786.67673895531
App 11783.5964391496
Arhgdib 2891.10323424149
Atg16l1 831.043188037807
Atm 147.667435005921
B2m 41553.4837735047
Batf 117.869073681856
Batf3 49.0017497329065
Bax 715.160671777555
Bcap31 3536.07221045569
Bcl2 151.64054984913
Bcl3 246.995306086137
Bcl6 719.795972427965
Bid 234.41377574931
Blnk 621.792472962152

Total number of rows: 547

Table truncated, full table size 10 Kbytes.




Supplementary file Size Download File type/resource
GSM6744009_20200320_Ray-chip1-MsImmunology-03-20-20_01_12.RCC.gz 6.5 Kb (ftp)(http) RCC
Processed data included within Sample table

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