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Sample GSM6222689 Query DataSets for GSM6222689
Status Public on Sep 27, 2023
Title Control 3
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
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 12.96924167
A_21_P0011517 20.77658833
A_22_P00006533 4.102268667
A_23_P250694 11.500305
A_23_P115316 1618.4255
A_21_P0010434 2.453647167
A_33_P3550618 7.5552115
A_33_P3244112 2.3959325
A_21_P0001775 128.9622333
A_22_P00025771 5.928475167
A_24_P701776 87.81133833
A_21_P0001716 81.17622833
A_22_P00009416 4.780069167
A_22_P00004115 7.922197167
A_22_P00009777 225.95055
A_23_P120103 2.218263
A_33_P3372389 29.22971667
A_21_P0010811 67.13302667
A_33_P6818098 605.6877
A_33_P3322539 48.07443

Total number of rows: 58201

Table truncated, full table size 1420 Kbytes.

Supplementary file Size Download File type/resource
GSM6222689_38730_257236339206_1_2.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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