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Sample GSM6744005 Query DataSets for GSM6744005
Status Public on Sep 22, 2023
Title Wild-type 8
Sample type RNA
 
Source name Subcutaneous myocardial matrix hydrogel injection and nearby dorsal skin
Organism Mus musculus
Characteristics Sex: male
strain: C57BL/6J: 000664
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.
wg2c
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 216.513330776207
Abcb1a 62.5482955575708
Abcf1 1054.90106161518
Abl1 353.638440267804
Adal 134.719405816306
Ahr 553.311845316973
App 11589.4774557153
Arhgdib 1710.45531313203
Atg16l1 645.931436815683
Atm 78.1853694469635
B2m 31022.7517447175
Batf 27.6655922658486
Batf3 49.3169253434693
Bax 632.700066601582
Bcap31 3096.14063009976
Bcl2 123.893739277496
Bcl3 58.939740044634
Bcl6 596.614511472214
Bid 114.270924576331
Blnk 522.037697538187

Total number of rows: 547

Table truncated, full table size 10 Kbytes.




Supplementary file Size Download File type/resource
GSM6744005_20200320_Ray2-MsImmun-03-20-20_01_12.RCC.gz 6.4 Kb (ftp)(http) RCC
Processed data included within Sample table

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