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Sample GSM6222691 Query DataSets for GSM6222691
Status Public on Sep 27, 2023
Title Vitiligo 4
Sample type RNA
Source name peripheral blood mononuclear cell
Organism Homo sapiens
Characteristics cell type: T cells
gender: female
subject status: Vitilogo patient
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 Vitiligo patients 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
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
VALUE normalized

Data table
A_24_P281036 11.05938933
A_21_P0011517 18.12858667
A_22_P00006533 2.093226
A_23_P250694 12.32114483
A_23_P115316 1330.592333
A_21_P0010434 2.017042333
A_33_P3550618 2.181313833
A_33_P3244112 2.304174667
A_21_P0001775 114.18305
A_22_P00025771 5.292436833
A_24_P701776 218.9944967
A_21_P0001716 71.44503667
A_22_P00009416 3.986515333
A_22_P00004115 6.585614333
A_22_P00009777 141.6652667
A_23_P120103 2.148984667
A_33_P3372389 39.992435
A_21_P0010811 73.96088
A_33_P6818098 663.5705667
A_33_P3322539 45.97618667

Total number of rows: 58201

Table truncated, full table size 1420 Kbytes.

Supplementary file Size Download File type/resource
GSM6222691_38734_257236339206_1_4.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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