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Sample GSM6039108 Query DataSets for GSM6039108
Status Public on Apr 01, 2024
Title Cortex_A1M_1dpi_rep3 [SAMPLE 39]
Sample type RNA
 
Source name Cortex, A1M, 1dpi, replicate3
Organism Mus musculus
Characteristics tissue type: Kidney cortex
treatment: A1M (5 mg/kg)
time: 1 day
Treatment protocol Samples of kidney medulla and kidney cortex were collected from mice that had received i.v. injection of a) 150 MBq 177Lu-octreotate and phosphate buffered saline solution (PBS), b) 5 mg/kg A1M and PBS, or c) 150 MBq 177Lu-octreotate and 5 mg/kg A1M. Samples were also collected from control mice that had received either two injections of PBS or PBS and A1M vehicle solution. Collection of the samples was performed at the time of death; three animals in each group were killed one day after injection and another three after seven days.
Extracted molecule total RNA
Extraction protocol According to the manufacturer's protocol, total RNA was extracted from frozen kidney tissue samples using the RNeasy Lipid Tissue Mini Kit (QIAGEN) or AllPrep® DNA/RNA/Protein Kit (QIAGEN). The purity, integrity and concentration of isolated RNA were assessed with Nanodrop 1000 Spectrometer (Thermo Scientific), RNA 6000 Nano LabChip Kit and Agilent 2100 Bioanalyzer (both from Agilent Technologies) and Qubit 3.0 Fluorometer (Thermo Fisher Scientific), respectively. Reverse transcription was performed from 200 ng total RNA using the RT2 First Strand Kit (QIAGEN).
Label SYBR Green
Label protocol For each reaction, a final volume of 25 µl was used which contained 12.5 µl of RT2 SYBR Green Mastermix (QIAGEN), 11.5 µl of nuclease free water and 1 µl of cDNA (1.7 µg of total RNA). Quantitative real-time PCR were performed (7500 Fast Real-120 Time PCR system, Applied Biosystem) with thermal profile starting by activation of HotStart DNA Taq polymerase at 95°C for 10 min followed by 40 cycles of 95°C for 15 sec and 60°C for 1min.
 
Hybridization protocol n/a
Scan protocol n/a
Description test
Data processing Sham-treated samples were used as a control. We compared the relative expression in kidney tissue between the controls and three treatment groups (177Lu-octreotate, 177Lu-octreotate+A1M, A1M) at one and seven days after administration. For data analysis, we used Microsoft Excel to calculate fold-expression of the target genes based upon the 2-ΔΔCt method (Livak and Schmittgen 2001). The relative expression compared to controls were analyzed by Welch T-test, and p<0.05 was considered significant. For differentially expressed genes in at least one group, one-way ANOVA followed by Welch T-test was used to determine significant differences between the 177Lu-octreotate, 177Lu-octreotate+A1M and A1M group. Target gene signals in all samples (test and controls) are normalized to geometric average of housekeeping genes provided in the same array, resulting in ΔCt values, where ΔCt=(Ct_Target-Ct_HKG). ΔCt values for all test replicates (at 1dpi and 7 dpi) were normalized against the average of corresponding control replicates, resulting in ΔΔCt, where ΔΔCt= ΔCt_test replicate– average ΔΔCt_control. 2^-ΔΔCT values for each condition were considered as fold change expression of test samples compared to controls (untreated). Fold change is determined for target genes in all replicates of test samples as 2^-ΔΔCt where -ΔΔCt= ΔCt_test replicate– average ΔΔCt_control
Non-normalized raw data matrix reports Ct values for target and housekeeping genes in all control and test replicates. Normalized Ct and fold change worksheet reports ΔCt and 2^-ΔΔCt, respectivly, calculates as indicated in the data processing
 
Submission date Apr 11, 2022
Last update date Apr 01, 2024
Contact name Charlotte Andersson
E-mail(s) charlotte.andersson@gu.se
Organization name University of Gothenburg
Department Department of Medical Radiation Science
Lab Forssell-Aronsson Lab
Street address Gula Stråket 2B
City Gothenburg
ZIP/Postal code 413 45
Country Sweden
 
Platform ID GPL32158
Series (1)
GSE200619 Real-time quantitative PCR analysis of mice kidney after administration of Lu-177-octreotate, Lu-177-octreotate + A1M and A1M

Data table header descriptions
ID_REF
VALUE Normalized Ct

Data table
ID_REF VALUE
1 6.469603299
2 2.55243945
3 3.386776685
4 2.435616254
5 7.528206586
6 2.795653104
7 5.073826551
8 3.990402936
9 1.784777402
10 4.813528775
11 5.226729154
12 3.967104673
13 4.556746244
14 6.42533946
15 9.92883563
16 2.556126355
17
18 7.097861051
19 5.177738904
20 3.83605647

Total number of rows: 84

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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