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Sample GSM4645082 Query DataSets for GSM4645082
Status Public on Aug 21, 2020
Title U87IL33 DNLS c4-4
Sample type RNA
 
Source name Mutant
Organism Mus musculus
Characteristics strain: SCID
age: 6-8 weeks
tissue: Brain
implanted cells: Human Glioma U87 expressing IL-33 DNLS
Treatment protocol U87pcDNA or U87 IL-33 or U87 IL-33 DNLS human glioma cells (5×10^4 cells/mouse) were implanted into the brain of mice by intracranial injection. Mice were monitored weekly. Animals bearing U87 tumors were sacrificed at 1 week after tumor implantation.
Growth protocol Six- to 8-week-old female SCID mice were housed in groups of three to five and maintained on a 12-hr light/dark schedule with a temperature of 22 °C±1 °C and a relative humidity of 50 ± 5%. Food and water were available ad libitum. All procedures were reviewed and approved by the University of Calgary Animal Care Committee. table transfectants of U87 or U251 cells were maintained in complete medium [Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% penicillin/streptomycin, 2 mM L-glutamine and 1 mM sodium pyruvate at 37ºC in a humidified 5% CO2 incubator. Cells were passaged by harvesting with Puck’s EDTA when they reached 80%–90% confluence.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from intracranial xenografts derived from U87pcDNA, IL-33 and DNLS cells. RNA was isolated using mirVana miRNA isolation kit (Ambion) according to the manufacturer's protocol. Total RNA purification to remove genomic DNA was carried out with Qiagen kit of RNeasy® Plus Micro following the manufacturer’s protocols. RNA Integrity Number (RIN) was assessed with RNA 6000 NanoChip on Agilent 2100 Bioanalyzer (Agilent Technologies).
Label Biotin
Label protocol 100 ng of total RNA in a final volume of 5 μl was mixed with a 3′ biotinylated capture probe and a 5′ reporter probe tagged with a fluorescent barcode from the nCounter Inflammation Panel (Mouse v2) gene expression code set.
 
Hybridization protocol Probes and target transcripts were hybridized overnight at 65°C for 16 hours per the manufacturer’s protocol. Hybridized samples were purified on the NanoString nCounter Prep Station using the high-sensitivity protocol, in which excess capture and reporter probes were removed and transcript-specific ternary complexes were immobilized on a streptavidin-coated cartridge.
Scan protocol The samples were scanned at maximum scan resolution on the nCounter Digital Analyzer.
Data processing Data analysis with nSolver software (NanoString Technologies). Samples that passed QC were further analyzed for fold change and normalized expression levels.
The expression levels of each gene were normalized, to both positive control probes and housekeeping genes built-in each probe set, by the nSolver Analysis Software.
 
Submission date Jun 29, 2020
Last update date Aug 22, 2020
Contact name Stephen M Robbins
E-mail(s) srobbins@ucalgary.ca
Phone (403) 220-4304
Organization name University of Calgary
Department Oncology
Lab HMRB 357
Street address 3330 Hospital Drive N.W.
City Calgary
State/province Alberta
ZIP/Postal code T2N 4N1
Country Canada
 
Platform ID GPL20885
Series (2)
GSE153488 Mouse immune cells response Interleukin-33 (IL-33) [nanostring]
GSE153489 Cerebral immune cells in the Interleukin-33 (IL-33) driven tumor microenvironment

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
Ager 1
Alox12 1
Alox15 2.64
Alox5 11.82
Areg 1
Arg1 7.23
Atf2 4125.45
Bcl2l1 1115.94
Bcl6 229.34
Birc2 428.5
C1qa 1563.84
C1qb 1538.14
C1ra 7.23
C1s 17.32
C2 52.2
C3 25.58
C3ar1 198.13
C4a 559.75
C6 1
C7 5.39

Total number of rows: 268

Table truncated, full table size 2 Kbytes.




Supplementary file Size Download File type/resource
GSM4645082_20170823_ASD20170823_20170823IL33_12.RCC.gz 3.1 Kb (ftp)(http) RCC
Processed data included within Sample table

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