|
| Status |
Public on Oct 30, 2015 |
| Title |
genomic DNA from Down syndrome Frontal Cortex glia 4 |
| Sample type |
genomic |
| |
|
| Source name |
Down syndrome Frontal Cortex glia 4
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
developmental stage: Adult
tissue: Frontal Cortex
cell type: Fluorescence-activated nuclei sorted glia
disease state: Down syndrome
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol. To distinguish 5mc from 5hmC in a subset of Down syndrome and control cerebellar cortices, bisulfite converted DNA and oxidative bisulfite converted DNA according to TrueMethylTM6 kit (CEGX) protocol was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip, in parallel.
|
| Scan protocol |
Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).
|
| Description |
Down syndrome glia Adult Frontal Cortex of patient 1139
tb6672
|
| Data processing |
Genome Studio software
For DS_processed_norm_no_batch_correction_no_filtering_matrix_1: normalized average beta values after background correction and normalization to internal controls (before ComBat batch adjustment and with no filtering)
For DS_processed_norm_batch_corrected_filtered_matrix_2: normalized average beta values after background correction and normalization to internal controls. In addition all probes mapping on the X or Y chromosome were removed along with those probes querying CpGs that overlapped common simple nucleotide polymorphisms (SNPs with minor allele frequency>1% in dbSNP build 138). Poorly performing probes with missing values (AVG_Beta detection p-value>.05) in more than 10% of the samples per subgroup were filtered out. We corrected for batch effect in the filtered probe sets using the ComBat R package including disease status in the adjustment model as an explanatory covariate, separately by tissue and cell type. ComBat adjustment requires at least 2 samples per batch. For each batch and tissue, probes with non missing values in less than 2 samples from the same subgroup were filtered out. These processed data correspond to the supplementary tables S3-S7 of the published manuscript.
For DS_OXBS_processed_matrix_3: BS values correspond to normalized average beta values (background correction and normalization to internal controls) after bisulfite treatment and OXBS values correspond to normalized average beta values after oxidative bisulfite treatment. In the manuscript, probes with detection p-values>0.005 in more than 1 sample were filtered out. These processed data correspond to the supplementary table S8 of the published manuscript.
For DS_raw_signal_matrix_1: unmethylated and methylated signal intensities without background correction and normalization to internal controls
For DS_OXBS_raw_signal_matrix_2: unmethylated and methylated signal intensities without background correction and normalization to internal controls. BS values correspond to intenstities in bisulifte treated DNA samples, OXBS values correspond to intenstities in oxidative bisulfite treated DNA samples.
|
| |
|
| Submission date |
Oct 29, 2015 |
| Last update date |
Oct 30, 2015 |
| Contact name |
Benjamin Tycko |
| E-mail(s) |
bejamintycko@hackensackmeridian.org
|
| Phone |
5519963595
|
| Organization name |
HUMC
|
| Department |
Epigenetics
|
| Street address |
40 prospect avenue
|
| City |
hackensack |
| State/province |
NJ |
| ZIP/Postal code |
07601 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE74486 |
Trans-effects of chromosome aneuploidies on DNA methylation patterns: DNA methylation analysis of Down syndrome in human brain tissues and cells |
| GSE74519 |
Trans-effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models |
|
