GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM6222688 Query DataSets for GSM6222688
Status Public on Sep 27, 2023
Title Control 2
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 10.83398133
A_21_P0011517 6.402608167
A_22_P00006533 5.259511667
A_23_P250694 2.114983
A_23_P115316 1197.047
A_21_P0010434 5.688988833
A_33_P3550618 6.517464
A_33_P3244112 3.792533833
A_21_P0001775 128.7326
A_22_P00025771 6.809363
A_24_P701776 82.988975
A_21_P0001716 69.59195167
A_22_P00009416 6.318885667
A_22_P00004115 8.668614667
A_22_P00009777 130.3349167
A_23_P120103 2.161499
A_33_P3372389 23.07759833
A_21_P0010811 84.583095
A_33_P6818098 323.0727167
A_33_P3322539 47.334455

Total number of rows: 58201

Table truncated, full table size 1420 Kbytes.

Supplementary file Size Download File type/resource
GSM6222688_38728_257236339206_1_1.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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