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Sample GSM6752760 Query DataSets for GSM6752760
Status Public on Jun 28, 2023
Title Liver_TAA_8W_rep3
Sample type RNA
 
Source name Liver_Wild type mice_8-week thioacetamide i.p.
Organism Mus musculus
Characteristics tissue: Liver
genotype: Wild type mice
age: 8-week
agent: thioacetamide i.p.
Treatment protocol Liver from liver fibrosis model induced by intraperitoneal injection of thioacetamide (TAA) in C57BL/6J mice for 8 weeks. Control mice received the same volume of normal saline (NS).
Extracted molecule total RNA
Extraction protocol The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Results were provided in Sample QC report.
Label Cy3
Label protocol Sample labeling was performed according to the manufacturer’s protocol (Arraystar Inc.). The circRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was 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 Array hybridization was performed according to the manufacturer’s protocol (Arraystar Inc.). 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 Axon GenePix 4000B microarray scanner (Molecular Devices, Inc.).
Description A total of 896 spot data on the Arraystar Mouse circRNA Array.
Data processing Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software 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 flag expressed(greater than 2 times background standard deviation) were retained for further analyses.
When comparing two groups or samples of profile differences, the “fold change” (i.e. the ratio of the group averages) between the groups or samples 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 ones.
 
Submission date Nov 22, 2022
Last update date Jun 28, 2023
Contact name shuaijie qian
E-mail(s) qsjbxh1997@outlook.com
Phone 13540675514
Organization name West China Hospital, Sichuan University
Lab Lab of Gastroenterology and Hepatology
Street address NO. 1, 4th Keyuan Road, Chengdu,
City chengdu
State/province sichuan
ZIP/Postal code 610041
Country China
 
Platform ID GPL32873
Series (2)
GSE218574 The angiogenic role of circRNA-007371 in liver fibrosis [circRNA Microarray]
GSE218581 The angiogenic role of circRNA-007371 in liver fibrosis

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
ASCRMP000515 8.744506098
ASCRMP001400 11.16501624
ASCRMP000684 6.5505104
ASCRMP001033 12.8566287
ASCRMP000656 8.986204695
ASCRMP001082 8.900235843
ASCRMP000777 10.75544332
ASCRMP000171 9.581085177
ASCRMP001074 6.037755412
ASCRMP001104 8.85461467
ASCRMP000991 7.730438467
ASCRMP000053 8.189017736
ASCRMP001682 7.770587887
ASCRMP001658 8.864010601
ASCRMP000608 9.291869415
ASCRMP000185 10.6283024
ASCRMP000670 9.303754176
ASCRMP001605 7.50414832
ASCRMP001669 7.235966708
ASCRMP001184 9.679004608

Total number of rows: 896

Table truncated, full table size 21 Kbytes.




Supplementary file Size Download File type/resource
GSM6752760_T44L.gpr.gz 548.1 Kb (ftp)(http) GPR
Processed data included within Sample table
Processed data are available on Series record

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