NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4445681 Query DataSets for GSM4445681
Status Public on Jun 23, 2020
Title BV_Ctrl_17 (circRNA)
Sample type RNA
 
Source name blood vessel, Ctrl
Organism Rattus norvegicus
Characteristics strain: Wistar
tissue: blood vessel
gender: male
age: 7 week
treatment: Ctrl
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.
Label Cy3
Label protocol Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.) Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).
 
Hybridization protocol The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.
Scan protocol The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.Scanned images were imported into Agilent Feature Extraction software for raw data extraction.
Data processing Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.
 
Submission date Mar 30, 2020
Last update date Jun 23, 2020
Contact name Jinghua Yang
E-mail(s) yangjh@xy-data.net
Organization name Beijing Zhiyun data technology co. LTD
Street address 32 North Third Ring Road West, Haidian District, Beijing
City Beijing
ZIP/Postal code 100098
Country China
 
Platform ID GPL21828
Series (2)
GSE147772 Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model [circRNA]
GSE147775 Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASCRPR000001 7.096895163
ASCRPR000002 7.584902983
ASCRPR000003 6.25251556
ASCRPR000004 8.436158004
ASCRPR000005 5.309870269
ASCRPR000006 7.243574638
ASCRPR000007 6.947690458
ASCRPR000008 7.754667603
ASCRPR000009 9.299247129
ASCRPR000010 7.990059018
ASCRPR000011 9.002652118
ASCRPR000012 8.003894969
ASCRPR000013 6.800150271
ASCRPR000014 9.113070347
ASCRPR000015 9.66647626
ASCRPR000016 6.63650977
ASCRPR000017 7.673076383
ASCRPR000018 6.090474065
ASCRPR000019 7.838838843
ASCRPR000020 7.415252304

Total number of rows: 14145

Table truncated, full table size 343 Kbytes.




Supplementary file Size Download File type/resource
GSM4445681_Ctrl_17.txt.gz 728.2 Kb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap