|
| Status |
Public on Dec 01, 2014 |
| Title |
Femoral plaque 79 |
| Sample type |
SRA |
| |
|
| Source name |
Femoral artery atherectomy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: athersclerotic human artery
gender: male
age: 78
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Purified chromosomal DNA was sonicated, methylated fragments captured by MethylCap kit (Diagenode AF-100-0048, Belgium) and sequenced
Multiplexed paired end ChIP protocol’ (Illumina): Sample Prep Master Mix Set 1 (NEB E6040) was used in combination with the Multiplexing Sample Preparation Oligo Kit (Illumina PE-400-1001) on Apollo 324 with PrepX-DNA Library Kit (IntegenX Cat# 400040)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
library strategy: MethylCap
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Paired end sequencing reads (51 bp) were mapped to human genome hg19 using Bowtie v0.12.9 software.3 The Bowtie parameters were set to 0 mismatches in the seed (first 28 nucleotides).
Only unique reads were retained and both fragments must be located within 400 bp of each other on the human reference genome hg19
Multiple paired reads with the exact same location in one sample were discarded, as these are most likely amplified from the same sequence
Methylated regions were annotated using Homo Sapiens Ensembl database v56.
Methylated regions were binned to promoter (from -2000 to +500 from transcription start site), exon (with exon number), intron and intergenic compartments
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: bed files, counts represent the highest number of overlapping reads observed in defined genomic locus. Length of loci varies from ~500 bp to ~3000 bp.
|
| |
|
| Submission date |
Dec 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Einari Aavik |
| Organization name |
University of Eastern Finland
|
| Department |
A.I. Virtanen Institute
|
| Street address |
Neulaniementie 2
|
| City |
Kuopio |
| ZIP/Postal code |
FIN-70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE53575 |
DNA methylation analysis of human atherosclerotic plaques in comparison to healthy mammary arteries |
|
| Relations |
| BioSample |
SAMN02484882 |
| SRA |
SRX397149 |
| Named Annotation |
GSM1296319_Femoral_79.bed.gz |
