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Sample GSM1954899 Query DataSets for GSM1954899
Status Public on Oct 12, 2016
Title ECSCs_12d_rep2
Sample type RNA
 
Source name endometriotic cyst stromal cells, 12 days, replicate2
Organism Homo sapiens
Characteristics cell type: endometriotic cyst stromal cells
gender: Female
age: 42y
treatment: 12d 10% charcoal-stripped heat-inactivated FBS
Treatment protocol ECSCs were obtained from premenopausal patients who had undergone salpingo-oophorectomy or cystectomy for ovarian endometriotic cysts. ECSCs were isolated from the corresponding tissues by enzymatic digestion. ECSCs were cultured in DMEM supplemented with 100 IU/ml of penicillin, 50 mg/ml of streptomycin, and 10% charcoal-stripped heat-inactivated fetal FBS at 37°C in 5% CO2 in air.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)
Label Cy3
Label protocol cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
 
Hybridization protocol cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.
Scan protocol The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
Description mRNA expression after 12d_10% charcoal-stripped heat-inactivated FBS
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.
 
Submission date Nov 25, 2015
Last update date Oct 12, 2016
Contact name yoko aoyagi
E-mail(s) yokoao@oita-u.ac.jp
Organization name oita university
Street address 1-1 Idaigaoka hamasamachi
City yufu city
ZIP/Postal code 879-5593
Country Japan
 
Platform ID GPL13497
Series (2)
GSE75423 mRNA expression profiles in decidualized and non-decidualized endometriotic cyst stromal cells (ECSCs).
GSE75427 Expression profiles in decidualized and non-decidualized endometriotic cyst stromal cells (ECSCs) and normal endometrial stromal cells (NESCs)

Data table header descriptions
ID_REF
VALUE quantile normalized signal, non-log scaled and ABS CALL.
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
A_23_P100001 172.500875 P
A_23_P100022 5.1880405 A
A_23_P100056 28.76403875 P
A_23_P100074 7313.44687 P
A_23_P100127 27.02527835 P
A_23_P100141 351.2842134 P
A_23_P100189 6.159693095 A
A_23_P100196 445.8095533 P
A_23_P100203 2414.31965 P
A_23_P100220 26.98289599 P
A_23_P100240 31.08359 P
A_23_P10025 5.256383283 A
A_23_P100292 9739.624865 P
A_23_P100315 2039.810875 P
A_23_P100326 5047.39653 P
A_23_P100344 127.8889762 P
A_23_P100355 1486.921045 P
A_23_P100386 5.083599257 A
A_23_P100392 1517.553422 P
A_23_P100420 1543.150464 P

Total number of rows: 34127

Table truncated, full table size 885 Kbytes.




Supplementary file Size Download File type/resource
GSM1954899_252665215262_S01_GE1_107_Sep09_1_2.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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