|
| Status |
Public on Dec 03, 2019 |
| Title |
202226400101_R07C01 |
| Sample type |
genomic |
| |
|
| Source name |
jejunum
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: crypt
age: 35
Sex: male
batch: 4
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted and purified using standard phenol-chloroform extraction with ethanol precipitation
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k or MethylationEPIC Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
jejunum crypt
|
| Data processing |
Data from 450k and EPIC IDAT files were read in separately with RnBeads and combined, only keeping the probes shared by the two platforms. Probes were filtered to remove those outside CpG contexts, in SNP, on the sex chromosomes, if they missing values, or if their standard deviation was below 0.005, indicating low variability. The greedy cut algorithm was used to remove probes with poor detection score p-values. After filtering of probes, data were normalized using BMIQ with the ENMix oob background correction method.
BMIQ and ENMix oob normalized beta values
|
| |
|
| Submission date |
Dec 02, 2019 |
| Last update date |
Dec 05, 2019 |
| Contact name |
Daniel Nachun |
| Organization name |
UCLA
|
| Lab |
Coppola
|
| Street address |
695 Charles E Young Dr S
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE141254 |
DNA methylation analysis validates organoids as a viable model for studying human intestinal aging (methylation) |
| GSE141256 |
DNA methylation analysis validates organoids as a viable model for studying human intestinal aging |
|
