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Sample GSM1266955 Query DataSets for GSM1266955
Status Public on Dec 11, 2013
Title GM00940_gDNA
Sample type genomic
 
Source name GM00940
Organism Homo sapiens
Characteristics gender: Female
cell type: primary skin fibroblast
population: Caucasian
Biomaterial provider http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM00940
Growth protocol The Fibroblast primary cell lines were grown in medium containing a-MEM (SigmaAldrich) supplemented with 2 mmol/l L-Glutamine, 100 U/mL penicillin, 100 mg/ml streptomycin, and 10% fetal bovine serum (SigmaAldrich) at 37°C with 5% CO2. At 70%-80% confluence, the cells were harvested.
Extracted molecule genomic DNA
Extraction protocol total RNA was extracted from cell lysates resuspended in 600 mL RLT lysis buffer using the Rneasy Mini Kit (Qiagen). DNA was extracted from cell lysates resuspended in 200 mL PBS using the GenElute DNA Miniprep Kit (SigmaAldrich).
Label Cy3 and Cy5
Label protocol according to manufacturer's instructions
 
Hybridization protocol according to manufacturer's instructions
Scan protocol according to manufacturer's instructions
Description Family 82, mother
Data processing Using GenomeStudio from Illumina
 
Submission date Nov 16, 2013
Last update date Dec 11, 2013
Contact name Tomi Markku Pastinen
E-mail(s) Tomi.Pastinen@mcgill.ca
Organization name McGill University and Génome Québec Innovation Centre
Street address 740, Dr. Penfield Avenue
City Montreal
State/province Quebec
ZIP/Postal code H3A 1A4
Country Canada
 
Platform ID GPL6984
Series (2)
GSE52442 The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts [genotyping]
GSE53261 The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts

Data table header descriptions
ID_REF
VALUE Genotype call
GM00940_gDNA.Score
GM00940_gDNA.Theta
GM00940_gDNA.R
GM00940_gDNA.B Allele Freq
GM00940_gDNA.Log R Ratio

Data table
ID_REF VALUE GM00940_gDNA.Score GM00940_gDNA.Theta GM00940_gDNA.R GM00940_gDNA.B Allele Freq GM00940_gDNA.Log R Ratio
200003-0_B_R_1526882017 AB 0.9299463 0.4531546 1.468286 0.5159964 0.1876449
200006-0_T_R_1526882018 AB 0.787675 0.444135 1.767623 0.4855427 -0.3004084
200047-0_B_R_1526882019 AA 0.8612435 0.08029316 0.6438069 0.04907291 0.3172884
200050-0_T_R_1526882020 BB 0.8331156 0.9865876 1.15029 0.9932337 -0.08747325
200052-0_B_R_1526882021 BB 0.9466458 0.9809607 1.024549 0.9911747 0.1373728
200053-0_B_F_1526882022 AA 0.7493879 0.1053558 1.234745 0.03158227 0.1511062
200070-0_B_F_1526882023 AB 0.9705294 0.5238703 0.6371677 0.5256908 0.2913249
200078-0_T_R_1526881818 AB 0.6531293 0.49692 2.372277 0.4688506 -0.004901309
200087-0_B_F_1526882024 AB 0.9078211 0.5200891 1.392139 0.4723117 0.1106534
200091-0_T_F_1526882025 AB 0.8204677 0.4860957 2.008426 0.4702805 -0.06147739
200096-0_T_F_1526882027 BB 0.9354096 0.9442673 0.9382958 0.9873143 -0.04711268
200124-0_B_R_1526882028 AA 0.8902165 0.03955407 0.8007951 0.01218575 0.07387825
200199-0_B_R_1526882030 AA 0.9598788 0.00 0.7305564 0.00 -0.007559663
200240-0_T_F_1526882031 AB 0.8782917 0.4746486 1.65638 0.5177546 0.08289456
200251-0_T_R_1526882032 AA 0.9409742 0.01819859 1.033367 0.005831875 0.05078711
200258-0_T_R_1526882033 AA 0.7451698 0.07268159 1.487258 0.0314397 -0.1869052
200260-0_B_F_1526881813 BB 0.7948331 0.9936352 1.380006 0.9888852 0.1076479
200261-0_T_R_1526882034 AA 0.8794336 0.08154464 1.249026 0.02109072 0.05560549
200262-0_B_F_1526882035 AB 0.9256892 0.4988003 0.837599 0.5392781 0.2041654
200519-0_B_R_1526882037 BB 0.8716854 0.9771309 1.317602 0.9886261 -0.2511669

Total number of rows: 1199187

Table truncated, full table size 95576 Kbytes.




Supplementary file Size Download File type/resource
GSM1266955_GM00940_gDNA_raw.txt.gz 19.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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