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Sample GSM6744007 Query DataSets for GSM6744007
Status Public on Sep 22, 2023
Title Deficient 2
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.
kme4c
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 169.418307103742
Abcb1a 86.1449019171568
Abcf1 758.07513687098
Abl1 343.143859303341
Adal 127.781604510449
Ahr 868.627760997997
App 12272.7770264643
Arhgdib 4605.88075583732
Atg16l1 541.277133712802
Atm 101.938133935302
B2m 72004.2162674555
Batf 142.139088163309
Batf3 111.988372492304
Bax 567.120604287949
Bcap31 3687.00180205431
Bcl2 145.010584893881
Bcl3 285.713924691903
Bcl6 730.795917930547
Bid 259.870454116756
Blnk 1042.3533131976

Total number of rows: 547

Table truncated, full table size 10 Kbytes.




Supplementary file Size Download File type/resource
GSM6744007_20200320_Ray-chip1-MsImmunology-03-20-20_01_10.RCC.gz 6.4 Kb (ftp)(http) RCC
Processed data included within Sample table

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