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Sample GSM3036864 Query DataSets for GSM3036864
Status Public on Mar 13, 2018
Title SAMPLE 87: female_O3_E_3h_rep4
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 -0.691
A2 -0.323
A3 -1.288
A4 0.471
A5 0.362
A6 -0.493
A7 0.736
A8 -0.647
A9 3.874
A10 2.928
A11 15.886
A12 -2.087
B1 6.657
B2 0.809
B3 4.392
B4 10.719
B5 3.393
B6 3.104
B7 5.867
B8 1.845

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

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