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Sample GSM6112202 Query DataSets for GSM6112202
Status Public on May 08, 2022
Title DS5_pan 10uM-F2
Sample type RNA
 
Source name DS5_pan
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: female
age: 3 months
cells: Cornea epithelia
tissue: Cornea
group: DS5_pan 10uM-F2
age (months): 2-3M
Treatment protocol Mice were exposed to desiccating stress (DS) conditions which included a drafty low humidity (<30% relative humidity) environment and received scopolamine in the drinking water (to inhibit tear secretion) . During DS, mice received twice a day eye drops of either vehicle, C1 or pan.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Qiagen mini plus columns according to the manufacturer's protocol. RNA quantity and quality was measured with NanoDrop and Bioanalyzer.
Label not provided
Label protocol not provided
 
Hybridization protocol One hundred nanograms of total RNA were hybridized with the NanoString Technologies nCounter Gene Expression GE- Mouse -Inflammation v2 Panel Codeset. Overnight hybridization occurred for 20 hours at 65°C. Removal of excess probes with magnetic bead purification was performed on the nCounter Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA structure was affinity purified by its 3’ end to remove excess reporter probes, then by its 5’ end to remove excess capture probes. Once unbound probes were washed away, the tripartite structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned by an electric current (negative to positive), and immobilized. Photobleaching and fluorophore degradation was prevented with the addition of SlowFade.
Scan protocol The cartridge containing immobilized samples was transferred to the nCounter Digital Analyzer (software v3.0.1.4) and scanned at 555 field of view (FOV). An epi-fluorescent microscope and CCD camera identified sets of fluorescent spots, which were tabulated for data output. Quality control metrics were recorded using the nSolver Analysis Software v4.0.6.2.
Data processing Data processing was analyzed with nCounter and ROSALIND software. Data in Matrix is after normalization by ROSALIND.
 
Submission date May 06, 2022
Last update date May 08, 2022
Contact name Cintia S. de Paiva
E-mail(s) cintiadp@bcm.edu
Phone 7137982124
Organization name Baylor College of Medicine
Department Ophthalmology
Lab de Paiva Lab
Street address 6565 Fannin Street NC505G
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL20885
Series (1)
GSE202378 New, Potent, Small Molecule Agonists of Tyrosine Kinase Receptors Improve Dry Eye Disease

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
AGER 4.456961564
ALOX12 9.416319579
ALOX15 10.5538231
ALOX5 4.608964657
AREG 8.331430682
ARG1 11.94881466
ATF2 10.63797574
BCL2L1 11.36117803
BCL6 7.496489928
BIRC2 10.54206513
C1QA 5.094391484
C1QB 4.094391484
C1RA 5.534964076
C1S 6.374499404
C2 4.608964657
C3 5.374499404
C3AR1 4.094391484
C4A 4.287036562
C6 4.094391484
C7 1.287036562

Total number of rows: 248

Table truncated, full table size 4 Kbytes.




Supplementary file Size Download File type/resource
GSM6112202_20210831_shn-DP-133041-NSXT-MmV2-Inflammation_DP25031_05.RCC.gz 3.2 Kb (ftp)(http) RCC
Processed data included within Sample table
Processed data are available on Series record

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