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Sample GSM6222690 Query DataSets for GSM6222690
Status Public on Sep 27, 2023
Title Control 4
Sample type RNA
 
Source name peripheral blood mononuclear cell
Organism Homo sapiens
Characteristics cell type: T cells
gender: female
subject status: heathly control
Treatment protocol Freshly drawn peripheral blood from healthy controls and vitiligo patinets. Leukocyte-enriched supernatants were separated using a Ficoll-Hypaque density gradient solution (specific gravity 1.077; Pharmacia Biotech, Uppsala, Sweden). The mononuclear cells were then aspirated from the interface, after centrifugation at 250 × g for 25 min. Finally, T cells were obtained using anti-human CD3-coated magnetic beads by the IMag Cell Separation System (BD Bioscience, Franklin Lakes, NJ, USA).
Extracted molecule total RNA
Extraction protocol Total RNA extraction was performed using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The extracted RNA was quantified by a ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) at OD260 nm and then qualitied by a Bioanalyzer 2100 (Agilent Technology, USA) using an RNA 6000 labchip kit (Agilent Technologies, Santa Clara, CA, USA).
Label Cy3
Label protocol 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.
 
Hybridization protocol 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.
Scan protocol After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.
Description T cells isolation from heathly controls PBMC
Data processing Scanned images are analyzed by Feature extraction10.7.3.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.
Raw signal data was normalized by quantile normalization for differential expressed genes discovering.
 
Submission date Jun 09, 2022
Last update date Sep 27, 2023
Contact name Hui Chun Yu
E-mail(s) junvsusagi@gmail.com
Phone +886920179628
Organization name Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation
Department Medical research
Street address No. 2, Min-Sheng Rd, Dalin Town
City Chia-Yi
ZIP/Postal code 62247
Country Taiwan
 
Platform ID GPL21185
Series (1)
GSE205751 Increased expression of LOC100506314 in T cells from patients with vitiligo and contributed to the pathogenesis of vitiligo

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
A_24_P281036 11.47622367
A_21_P0011517 14.46049167
A_22_P00006533 2.689404833
A_23_P250694 11.57377217
A_23_P115316 1313.644748
A_21_P0010434 2.234132833
A_33_P3550618 2.143880833
A_33_P3244112 2.180128667
A_21_P0001775 152.81075
A_22_P00025771 6.606005167
A_24_P701776 105.0155183
A_21_P0001716 80.91359333
A_22_P00009416 3.841934667
A_22_P00004115 3.604261333
A_22_P00009777 170.2675
A_23_P120103 2.122146167
A_33_P3372389 39.488555
A_21_P0010811 70.08069833
A_33_P6818098 618.3578
A_33_P3322539 44.09091667

Total number of rows: 58201

Table truncated, full table size 1420 Kbytes.




Supplementary file Size Download File type/resource
GSM6222690_38732_257236339206_1_3.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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