NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3036844 Query DataSets for GSM3036844
Status Public on Mar 13, 2018
Title SAMPLE 34: female_O3_E_3h_rep3
Sample type RNA
 
Source name female mouse exposed to 2ppm ozone
Organism Mus musculus
Characteristics tissue: lung tissue homogenate
exposure time: 3 hours
Sex: female
estrous cycle stage: estrus
Treatment protocol Male and female C57BL/6 mice of 8 weeks of age were exposed to 2ppm ozone (O3) or filtered air (FA) for 3 hours. Females were exposed at different stages of the estrous cycle: diestrus 1 (D1), diestrus 2 (D2), proestrus (P), estrus (E). Total RNA was extracted from whole lung homogenates and PCR arrays were used to determine the expression of 84 miRNAs associated with inflammation and immunity (3-9 animals per condition).
Extracted molecule total RNA
Extraction protocol Lung tissue was homogenized in Trizol. Total RNA was extracted with the Direct-zol (Zymo Research)
Label SYBR Green
Label protocol Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 84 mouse miRNAs predicted to regulate inflammatory genes was assayed with the Mouse Inflammatory Response & Autoimmunity miRNA PCR Array (MIMM-105Z, Qiagen)
 
Hybridization protocol n/a
Scan protocol n/a
Data processing Data were analyzed in excel using Ct values for each sample, normalized to he average Ct of five miRNA housekeeping controls (SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A, RNU6-2)
Matrix normalized template shows target miRNA Ct values normalized to housekeeping miRNAs as ΔCt = (Ct_Target − Ct_housekeeping)
For fold change calculations, ΔΔCt based fold-change values were obtained using sample 27 as control (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])). A fold change of 200 was considered as cutoff.
 
Submission date Mar 12, 2018
Last update date Mar 13, 2018
Contact name Patricia Silveyra
E-mail(s) psilveyr@iu.edu, ptrcslvr@gmail.com
Organization name Indiana University Bloomington
Department Environmental and Occupational Health
Lab Silveyra lab
Street address 2819 E 10th St
City Bloomington
State/province Indiana
ZIP/Postal code 47408
Country USA
 
Platform ID GPL24720
Series (1)
GSE111667 miRNA expression in lung tissue

Data table header descriptions
ID_REF
VALUE Matrix non-normalized are raw Ct values. Matrix normalized are normalized to the average of housekeeping miRNAs (H3:H8). Fold changes are calculated with the livak method (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])

Data table
ID_REF VALUE
A1 -0.725
A2 -0.406
A3 -1.389
A4 0.349
A5 0.257
A6 -0.374
A7 1.039
A8 -0.179
A9 3.385
A10 2.684
A11 16.155
A12 -1.993
B1 7.108
B2 0.725
B3 4.245
B4 11.008
B5 3.830
B6 3.497
B7 5.908
B8 1.982

Total number of rows: 96

Table truncated, full table size <1 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap