NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2195414 Query DataSets for GSM2195414
Status Public on Jun 10, 2016
Title normal FLSs 2
Sample type RNA
 
Source name fibroblast-like synoviocytes from trauma patient
Organism Homo sapiens
Characteristics subject status: trauma patient
Sex: female
age: 47 years
cell type: fibroblast-like synoviocytes
Growth protocol Tissue specimens were minced into small pieces and digested for 2 hours with 2 mg/ml of type II collagenase (Invitrogen, Carlsbad, CA, USA) in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) at 37°C. After centrifugation at 210 × g for 5 minutes, the precipitate was resuspended with 1 ml of high-glucose DMEM containing 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 units/ml streptomycin, and then cultured in 25-cm2 cell culture flasks (Corning) in a humidified 5% CO2 incubator. After 10 hours, 4 ml of high-glucose DMEM containing 10% FBS was added to the cell culture flask. All experiments were conducted using cells at passage 3.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from fibroblast-like synoviocytes using Agient total RNA isolation Mini kit (Agilent Technologies, Santa Clara, CA, USA) following the manufacture's recommended protocol. The quality and the concentration of the RNA samples were monitored at absorbance ratios of A260/A280 and A260/A230 using a NanoDrop 8000 spectrophotometer.
Label Cy3
Label protocol Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. 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, heated to 60 °C for 30 min, and diluted with 25 μl 2 × GE hybridization buffer. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the Human LncRNA Array v3.0 slide (8 x 60K, Arraystar). The slides were incubated for 17 hours at 65°C in an Agilent hybridization oven then washed, fixed and scanned.
Scan protocol The slides were scanned using the Agilent DNA Microarray Scanner (part number G2505C).
Description lncRNAs and mRNAs expression
normal 2
Data processing The scanned were images were analysed using the Agilent Feature Extraction software version 11.0.1.1. Data normalization was carried out using Agilent GeneSpring GX. After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs between two groups were identified through Volcano Plot filtering.
 
Submission date Jun 09, 2016
Last update date Jun 10, 2016
Contact name Yu Zhang
E-mail(s) zhangyu00110011@126.com
Phone +86-15751011866
Organization name Jinling Hospital
Department Clinical Laboratory Science
Street address 305 East Zhongshan Road
City Nanjing
State/province Jiangsu
ZIP/Postal code 210002
Country China
 
Platform ID GPL16956
Series (1)
GSE83147 RNA expression profiles in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P058197 2.3315904
ASHGA5P007773 8.009256
ASHGA5P031162 3.1662462
ASHGA5P041796 13.945251
ASHGA5P006930 7.574936
ASHGA5P031496 7.3432627
ASHGA5P050699 12.806125
ASHGA5P035298 3.1332583
ASHGA5P014867 3.8678212
ASHGA5P008172 3.9325845
ASHGA5P047663 4.2662477
ASHGA5P012016 5.5494113
ASHGA5P007747 9.350673
ASHGA5P026943 2.622485
ASHGA5P035562 4.206131
ASHGA5P018786 10.672335
ASHGA5P001180 5.7062836
ASHGA5P023786 2.8541749
ASHGA5P021269 3.9534369
ASHGA5P000239 4.2064285

Total number of rows: 58944

Table truncated, full table size 1360 Kbytes.




Supplementary file Size Download File type/resource
GSM2195414_normal2.txt.gz 2.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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