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Sample GSM7122517 Query DataSets for GSM7122517
Status Public on Apr 20, 2024
Title NM1
Sample type RNA
Source name Total RNA from human bile exosome samples
Organism Homo sapiens
Characteristics tissue: bile exosome
disease: benign biliary obstruction
patient: patient No.1
Extracted molecule total RNA
Extraction protocol Bile samples were obtained from patients undergoing preoperative biliary drainage, collected within 6 hours after emptying the drainage bag and immediately stored at -80℃ until further processing and testing. The isolation of exosomes was conducted via differential ultracentrifugation. Total RNA was extracted using an improved TRIzol-based method.
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). 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.
Hybridization protocol 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.
Scan protocol The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.
Data processing Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 5 out of 10 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 2.0 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.
The significantly differentially expressed circRNAs were defined as normalized log2 ratios>1.5 and p-values <= 0.05).
Submission date Mar 29, 2023
Last update date Apr 20, 2024
Contact name Ningyuan Wen
Organization name West China Hospital, Sichuan University
Street address No.37 GuoXueXiang, Wuhou district, Chengdu, China
City Chengdu
ZIP/Postal code 610041
Country China
Platform ID GPL21825
Series (1)
GSE228477 An exosomal circRNA signature in the diagnosis and prognostification of cholangiocarcinoma: circRNA microarray analysis for 10 human bile samples

Data table header descriptions
VALUE normalized signal

Data table
ASCRP3000001 5.441428899
ASCRP3000002 11.38389578
ASCRP3000003 8.10318118
ASCRP3000004 5.751500289
ASCRP3000005 6.662201074
ASCRP3000006 5.691447726
ASCRP3000007 6.520497377
ASCRP3000008 6.832949194
ASCRP3000009 5.399592183
ASCRP3000010 5.328094442
ASCRP3000011 6.54928004
ASCRP3000012 5.910819649
ASCRP3000013 7.650008236
ASCRP3000014 5.597999533
ASCRP3000015 9.628180628
ASCRP3000016 7.319940096
ASCRP3000017 5.551243379
ASCRP3000018 5.498165409
ASCRP3000019 6.491930256
ASCRP3000020 5.230253362

Total number of rows: 13617

Table truncated, full table size 330 Kbytes.

Supplementary file Size Download File type/resource
GSM7122517_NM1.txt.gz 715.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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