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Sample GSM7038889 Query DataSets for GSM7038889
Status Public on Jun 14, 2023
Title Control 4
Sample type RNA
 
Source name cardiac left ventricle
Organism Mus musculus
Characteristics strain: C57Bl/6
Sex: Male
age: 3-4 months
treatment: sham
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
E-mail(s) meghbali@g.ucla.edu
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
ID_REF
VALUE normalized signal intensity

Data table
ID_REF VALUE
1001 10.23132536
1002 5.398684697
1003 6.435027833
1008 6.641226213
1009 6.562377528
1012 8.074756993
1014 9.881608995
1015 10.28623001
1021 6.273232353
1022 16.39176947
1026 7.545899742
1028 6.105649774
1030 16.39184294
1032 7.00992307
1033 16.39179886
1037 5.673494175
1038 4.961370028
1042 6.066297853
1044 16.39183559
1047 5.715128671

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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