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Sample GSM986955 Query DataSets for GSM986955
Status Public on Aug 24, 2012
Title BA10 CTRL 1003 MspI
Sample type genomic
Source name Frontal cortex of the brain (BA10)
Organism Homo sapiens
Characteristics age (y): 51-60
Sex: F
post-mortem interval: 51
tissue: Frontal cortex of the brain (BA10)
disease state: control
enzymatic digestion: 200 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.
Treatment protocol No treatment for human and mouse tissues. Only one human cell line underwent SAHA treatment protocol; stated in the sample description.
Growth protocol Human and mouse untreated tissues were analyzed in this study
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted applying standard phenol chloroform and isopropanol precipitation method. Genomic DNA was then sheared to 200bp fragment length on Covaris S2 sonifier (Covaris, USA); blunt ended and ligated to adaptors before subjecting for glucosylation and restriction enzyme digestion. Glucosylation reaction was performed in presence of 200 µM uridine-5’-diphospho-α -D-glucose (UDP-Glc, Sigma) and 80ng BGT (Lariviere, Kurzeck et al. 2002) in 100mM Tris-HCl (pH 8.0) and 25mM MgCl2 for 3 h at 37ºC.
Label biotin
Label protocol 9 ug of PCR amplified DNA products were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments
Hybridization protocol Approximately 9 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. All array sets were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.
Scan protocol Arrays were scanned on an Affymetrix Gene Chip Scanner 3000 7G
Description Post-mortem brain samples (BA10) of individuals with no diagnosis of major psychosis. Databanks: Stanley & Maclean
Data processing We distinguished between three types of probes on the tiling microarray: “target probes”, which contain the restriction site CCGG, “flanking probes”, which do not contain the recognition sequence but could lie up to 200 bp upstream or downstream of a target probe (sheared DNA fragments were of average 200 bp), and “non-target probes” that neither contain a target sequence nor are within 200 bp (on either side) of the target sequence. After comparing different array preprocessing algorithms, we chose to use a sequence-based algorithm after Potter et al (Supplementary Note). The model (Supplementary Note, equation 1) was applied to non-target probes matched proportionally to target probes by GC content. Normalized intensities were obtained by subtracting the fitted value from raw probe intensities, resulting in a normal distribution of probe-level intensities. Each chip was independently normalized. All downstream analyses were carried out at the single-probe level (i.e. without windowing or peak-calling) and solely on target probes. Probes overlapping repeats were excluded. Probes were required to have a ‘CCGG’ in both the Affymetrix probe sequence and the chromosomal sequence downloaded from UCSC; probes that did not meet this criterion were excluded.
EXP2_Human_BrainLiver_sample_metadata.xls, HumanBrain_sample_metadata.xls
BED files of normalized intensities for target probes. Unless otherwise specified, probes overlapping repeats are excluded. Unless otherwise specified, target probes that did not contain a CCGG in the UCSC genome sequence were also excluded.
Submission date Aug 16, 2012
Last update date Aug 24, 2012
Contact name Shraddha Pai
Organization name University of Toronto
Street address 160 College Street, Room 602
City Toronto
State/province ON
ZIP/Postal code M5S 3E1
Country Canada
Platform ID GPL4914
Series (2)
GSE40166 5-hmC in the brain: abundance in synaptic genes and differences at the exon-intron boundary (tiling array)
GSE40167 5-hmC in the brain: abundance in synaptic genes and differences at the exon-intron boundary

Supplementary file Size Download File type/resource
GSM986955_BA10_CTRL_1003_MspI.bed.gz 756.4 Kb (ftp)(http) BED
GSM986955_BA10_CTRL_1003_MspI_D12_Hs35b_P05R_v01_.CEL.gz 22.0 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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