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Sample GSM2044368 Query DataSets for GSM2044368
Status Public on Aug 01, 2016
Title PBMC_ASD_rep2
Sample type RNA
 
Source name PBMC, autistic infant, replicate 2
Organism Homo sapiens
Characteristics diagnosis: autism
tissue: whole blood
cell type: PBMC
Growth protocol PBMC was isolated by density gradient centrifugation on Percoll (d = 1.077) .
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions and purified by RNeasy MinElute Cleanup kit.
Label Cy3
Label protocol Complementary DNA amplification was carried out from 35 ng of total RNA using an Ovation PicoSL WTA System V2. After amplification, cDNA samples were labeled with Cy3 using Klenow polymerase.
 
Hybridization protocol Slide was hybridized with 1.65 μg Cy3-labeled cDNA using a Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, USA) in a hybridization oven.
Scan protocol After 17 h of hybridization at 65 °C, the slide was washed with a Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.
Data processing The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The intensity signals was imported to CLC Main workbench 6.0 and normalized by the quartile normalization method and log2 transformed.
 
Submission date Jan 21, 2016
Last update date Aug 01, 2016
Contact name Ryo Inoue
E-mail(s) r-inoue@kpu.ac.jp
Organization name Kyoto Prefectural University
Street address 1-5, Hangi-cho, shimogamo
City Kyoto
ZIP/Postal code 606-8522
Country Japan
 
Platform ID GPL17077
Series (1)
GSE77103 Gene expression in peripheral blood mononuclear cells from healthy control and autistic infants

Data table header descriptions
ID_REF
VALUE normalized log2 transformed

Data table
ID_REF VALUE
A_23_P11507 7.101066052
A_33_P3319026 7.519765294
A_24_P282108 6.698482808
A_23_P254888 7.63707079
A_23_P426140 6.278148275
A_24_P49533 5.244598976
A_32_P132589 1.592292695
A_33_P3256490 2.061665529
A_23_P303317 2.237740985
A_33_P3295423 6.094482771
A_33_P3334308 7.86408088
A_23_P502627 4.528051077
A_23_P63789 6.739733447
A_33_P3212994 5.680426936
A_33_P3433873 6.171147293
A_23_P64204 6.852888882
A_32_P109522 5.637743435
A_33_P3416420 5.029356143
A_21_P0000778 4.941057997
A_33_P3252989 9.289856592

Total number of rows: 50599

Table truncated, full table size 1255 Kbytes.




Supplementary file Size Download File type/resource
GSM2044368_A3.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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