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Sample GSM6797920 Query DataSets for GSM6797920
Status Public on Dec 07, 2022
Title Young RVLM, set1, biological replicate 5
Sample type RNA
 
Source name Rostral ventrolateral medulla, Young
Organism Rattus norvegicus
Characteristics strain: Fischer 344
gender: Male
weight: 319 g
developmental stage: Young
tissue: RVLM
Treatment protocol n/a
Growth protocol n/a
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Rneasy Lipid tissue Mini Kit followed by DNase I treatment.
Label SYBR Green
Label protocol Fifty ng of RNA from each sample was reverse transcribed and preamplified using an RT2 preamp cDNA synthesis kit (Qiagen, Inc.) with PBR-152Z RT2 preamp pathway primer mix (Qiagen, Inc.). Quantitative polymerase chain reactions were performed on these preamplified samples on StepOnePlus master cycler (Applied Biosystems™, Thermo Fisher Scientific) using Rat GABA & Glutamate RT2 Profiler PCR arrays (Qiagen, Inc., GeneGlobe ID PARN-152Z) with SYBR Green ROX qPCR master mix (Qiagen, Inc.,).
 
Hybridization protocol n/a
Scan protocol n/a
Description Young RVLM
Young 1503056
Data processing Matrix non-normalized: To calculate threshold cycle (Ct) values, the background fluorescence of each well was identified by setting the start of baseline at cycle 3 and the end of baseline at cycle 15 for each array plate. The threshold value for Ct was manually selected, and the same threshold value (1.52) was used for all the arrays. After threshold selection, the Ct values of each array plate were exported as an Excel file. StepOnePlus software (Applied Biosystems) was used for Ct values extraction.
Matrix normalized: The Ct values for three of the five housekeeping genes (B2m, Hprt1, and Rplp1) were identified to be consistent between arrays and were therefore used as reference genes for normalizing RNA expression. The geometric mean of the B2m, Hprt1, and Rplp1 Ct values for each experimental RVLM sample/array was used for the ΔCt value calculation of each gene. Normalization process was performed in Microsoft Excel. Genes that showed <30 Ct value in more than 50% of the arrays were used in the final analysis. Seventy-nine of the 84 GABA and glutamate neurotransmission-related genes met these criteria. In contrast, Avp, Gabra6, Gabrr1, Grm6, and Slc1a7 genes did not meet these criteria and were removed from the final analysis. Target gene signal normalized to geometric mean of B2m, Hprt1, and Rplp1 reference genes signal; 2–ΔCt, where –ΔCt = –(Ct_Target –geometric mean of B2m, Hprt1, and Rplp1 reference genes Ct values). See Data table below.
Fold Change: Aged vs. young, aged vs. middle-aged, and middle-aged vs. young rats RVLM gene expression differences are represented as fold change values calculated using the 2–ΔΔCt method (Livak and Schmittgen, 2001). Fold change calculations were performed in Microsoft Excel.
 
Submission date Dec 07, 2022
Last update date Dec 07, 2022
Contact name Sivasai Balivada
E-mail(s) sbalivada@utep.edu
Phone 7854777070
Organization name University of Texas at El Paso
Street address 4th floor, Bioscience research building
City El Paso
State/province Texas
ZIP/Postal code 79968
Country USA
 
Platform ID GPL32921
Series (1)
GSE220296 Age-associated downregulation of glutamate and GABA neurotransmission-related gene expression in the rostral ventrolateral medulla of male Fischer 344 rats

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
A01 0.425380956
A02 0.030808575
A03 0.124226573
A04 0.004149593
A05 0.071396176
A06 3.076390142
A07 null
A08 0.001845175
A09 0.017074551
A10 0.008196253
A11 0.057712501
A12 0.014225515
B01 0.109410127
B02 0.470338256
B03 0.192544408
B04 0.048264825
B05 0.106444124
B06 0.007250205
B07 0.094281931
B08 null

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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