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Sample GSM5627753 Query DataSets for GSM5627753
Status Public on Oct 15, 2021
Title Orbital adipose/connective tissue_excised_rep1
Sample type RNA
Source name Orbital adipose/connective tissue from orbital decompression surgery
Organism Homo sapiens
Characteristics diagnosis: Thyroid-associated ophthalmopathy (TAO)
tissue: Orbital adipose/connective tissue
gender: Female
Stage: Stable period
Growth protocol Liquid nitrogen quick freezing, -80 degrees refrigerator storage.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted and purified using RNeasy micro kit and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100.
Label Cy3
Label protocol Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions.
Hybridization protocol Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat.# 5188-5327, Agilent Technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.
Scan protocol Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US).
Description TAO 1
Data processing Raw data were normalized by Quantile algorithm, limma packages in R.
After the original data were normalized with the limma package in the software R, the differential genes were screened using Fold-change (fold of expression difference) and T-test (Student's t-test) statistical methods, and the selection conditions were as follows: 1) Fold Change (linear) =< 0.5 or Fold Change (linear) >= 2. 2) T-test p-value <0.05 or <0.01.
Submission date Oct 14, 2021
Last update date Dec 30, 2021
Contact name Zifan Yue
Phone 15821673019
Organization name Shanghai Changzheng Hospital
Department Ophthalmology
Street address No. 415 Fengyang Road, Hangpu District
City Shanghai
ZIP/Postal code 200001
Country China
Platform ID GPL30862
Series (1)
GSE185952 For lncRNA, circRNA and mRNA sequencing of thyroid-associated ophthalmopathy patients and normal people

Data table header descriptions
VALUE Normalized value

Data table
A_22_P00001056 1.938031047
CUST_25733_PI448380708 5.877778068
CUST_38665_PI448380708 4.887562881
A_23_P409516 8.773736222
CUST_76915_PI448380708 7.23432216
CUST_33809_PI448380708 4.318592699
A_23_P34018 15.10316819
A_24_P188941 14.72938282
CUST_20427_PI448301858 9.437738308
CUST_18337_PI448380708 5.285127526
CUST_1104_PI448301858 4.949100503
CUST_15263_PI448380708 6.949089625
CUST_42174_PI448380708 9.466353109
A_33_P3279969 5.785540264
CUST_105349_PI448380708 7.140400008
CUST_16722_PI448380708 12.80553269
CUST_22908_PI448380708 6.798430261
CUST_24735_PI448380708 1.466216156
A_33_P3317431 13.06124036
CUST_65766_PI448380708 4.567200836

Total number of rows: 173079

Table truncated, full table size 5557 Kbytes.

Supplementary file Size Download File type/resource
GSM5627753_597033_258636010008_S001_GE1_1200_Jun14_1_2.txt.gz 24.5 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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