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Sample GSM7038896 Query DataSets for GSM7038896
Status Public on Jun 14, 2023
Title HF-ESTR 2
Sample type RNA
Source name cardiac left ventricle
Organism Mus musculus
Characteristics strain: C57Bl/6
Sex: Male
age: 3-4 months
treatment: Transverse aortic constriction + 10‐day continuous‐release pellet of 0.03 mg Estradiol/kg per day
Treatment protocol Healthy mice with an ejection fraction of ˜60% were randomly subjected to sham or transaortic constriction (TAC) surgery as described previously. HF was achieved 6 to 8 weeks after the TAC surgery with an ejection fraction of ˜35%. Once TAC mice reached HF, mice were randomly euthanized (HF group), or were assigned to treatment of estradiol (E2) via a subcutaneous 10-day continuous-release pellet of 0.03 mg E2/kg per day (Innovative Research of America, )
Extracted molecule total RNA
Extraction protocol For RNA extraction, hearts were powdered with a mortar and pestle on dry ice, suspended in Trizol (Invitrogen), and homogenized with a Polytron (Kinematica). Total RNA was isolated using Trizol according to manufacturer instructions. Quality control of the total RNA samples was assessed using gel electrophoresis. The samples sent to Ocean Ridge Biosciences were checked for quality by Bioanalyzer on Agilent 2100 Bioanalyzer RNA 6000 Pico Chip(s).
Label Oyster-550 fluorescent dye
Label protocol The total RNA was DNase digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).
Hybridization protocol Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.
Scan protocol The microarrays were scanned on an Axon GenePix 4000B scanner, and data was extracted from images using GenePix V4.1 software.
Data processing Raw data was background-subtracted, Log2-untransformed, and normalized. Intensity for each oligo probe is based on averaging of triplicate spots. Normalized threshold is calculated based on: log2(5* stdev of negative controls) + trim mean (log2-transformed negative control probe signals). Normalized Factor is the averge value of 20% Trim MeanNormalized TPT95 is calculated based on 95th percentile of negative control probe signal
Submission date Feb 10, 2023
Last update date Jun 14, 2023
Contact name Mansoureh Eghbali
Organization name UCLA David Geffen School of Medicine
Street address 10833 Le Conte Ave
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platform ID GPL33116
Series (1)
GSE225067 Cardiac miRNA profiling in mouse heart failure that is rescued by estrogen treatment .

Data table header descriptions
VALUE normalized signal intensity

Data table
1001 10.14952603
1002 5.849873698
1003 6.166239997
1008 6.729327763
1009 6.427772992
1012 7.944467269
1014 10.4704543
1015 10.30786717
1021 6.147279423
1022 16.32520041
1026 7.013706024
1028 5.917532021
1030 16.32514899
1032 6.68376578
1033 16.32520776
1037 5.403059171
1038 4.837896185
1042 6.174382961
1044 16.32511226
1047 5.334242212

Total number of rows: 2576

Table truncated, full table size 54 Kbytes.

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

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