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| Status |
Public on Oct 18, 2013 |
| Title |
GM18502_cDNA_HumanOmni2.5-Quad |
| Sample type |
RNA |
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| Source name |
GM18502_cDNA
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| Organism |
Homo sapiens |
| Characteristics |
gender: female
tissue: Lymphoblasts
population: YRI
assayed molecule: cDNA
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| Biomaterial provider |
YRI_LCL HapMap
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| Treatment protocol |
Approximately 150µg of total RNA was extracted from the cells using the commercially available TRIzol reagent protocol (Invitrogen, Burlington, ON, CA) and subsequently treated with 18 U DNaseI (Ambion Inc., Austin, TX, USA) for 30 min at 37°C and further extracted with phenol/chloroform. High RNA quality was confirmed for all samples using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA, USA) and the concentrations were determined using the NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA). Poly(A) RNA was then isolated using the MicroPoly(A)Purist protocol (Ambion Inc., Austin, Tx, USA) and poly-A enriched RNA quality and quantity was measured using the Agilent 2100 BioAnalyzer and NanoDrop ND-1000, respectively.
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| Growth protocol |
All cells were obtained from the Coriell Institute for Medical Research (Camden, NJ). The LCLs were grown in T75 flasks in 1X RPMI 1640 Media (invitrogen, Burlington, ON), with 2 mM L-glutamine, 15% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2. LCL cells were harvested during log growth phase. The Fibroblast primary cell lines were immortalized as previously desribed (Grundberg et al., PLoS Genet., 2011), and then 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, fibroblast cells were harvested.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA and gDNA were extracted from cell lysates and we applied a cDNA synthesis protocol as previously described in Moros et al., Genome Biology, 2011 (PMID: 21418647).
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| Label |
Cy3 and Cy5
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| Label protocol |
according to manufacturer's instructions
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| Hybridization protocol |
according to manufacturer's instructions
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| Scan protocol |
according to manufacturer's instructions
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| Description |
YRI Family #004- Mother
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| Data processing |
GenomeStudio from Illumina
For convenience, data was compiled based on analysis date into 20 individual sets.
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| Submission date |
Sep 30, 2013 |
| Last update date |
Jan 14, 2014 |
| Contact name |
Tomi Pastinen |
| E-mail(s) |
[email protected]
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| Organization name |
McGill University
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| Department |
Human & Medical Genetics
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| Street address |
740 Dr Penfield
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| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3A0G1 |
| Country |
Canada |
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| Platform ID |
GPL13314 |
| Series (1) |
| GSE51272 |
Genome-wide characterization of allelic chromatin in human fibroblast and lymphoblastoid cell lines by high-density allele-specific analyses |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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