|
| Status |
Public on Dec 20, 2019 |
| Title |
genomic DNA from HBMVECs in EBM plus angiogenic growth factors_B1 |
| Sample type |
genomic |
| |
|
| Source name |
EGM1_zappulliMGH1_B1
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: normal
cell type: HBMVECS
protocol: 16 hours on Matrigel with angiogenic growth factors in Basal medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNAs for methylation analysis were purified (Qiagen QIAamp® DNA Micro Kit, Qiagen,Stanford, CA, USA)
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Illumina Cy3 and Cy5
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
Cell pellet from medium (floating cells) and Matrigel (dispase treated and resuspended)
|
| Data processing |
Illumina Human 450K Infinium Methylation BeadChip beta values from GenomeStudio were input to RnBeads [version 2.0.1] with annotations from RnBeads.hg19 [version 1.14.0] (Assenov et. al., 2014) in R [version 3.5.1]. Filtering removed probes annotated as non-CpG, cross-reactive, snp-containing, or on sex chromosomes. Probes with variance of less than .05 across all samples were excluded.
|
| |
|
| Submission date |
Sep 23, 2019 |
| Last update date |
Dec 20, 2019 |
| Contact name |
Aleksandar Milosavljevic |
| E-mail(s) |
amilosav@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Department |
Genetics and Genomics
|
| Lab |
Bioinformatics Research Laboratory
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE137830 |
Glioma-derived miRNA-containing extracellular vesicles induce angiogenesis by reprogramming brain endothelial cells (DNA methylation) |
| GSE138115 |
Glioma-derived miRNA-containing extracellular vesicles induce angiogenesis by reprogramming brain endothelial cells |
|
