|
| Status |
Public on Apr 08, 2014 |
| Title |
T1DS DNaseI Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
twin 1_T21_fetal primary fibroblasts_DNaseI
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Trisomy 21
tissue: Fetal primary fibroblasts
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Refer to the Nuclei isolation section of John et.al. Current Protocols in Molecular Biology PMID: 23821440
Illumina TruSeq v2
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 1
|
| Data processing |
Basecalls performed with Illumina RTA version 1.12.4.2
Illumina chastity filtered reads were aligned to the Human GRCh37/hg19 reference with bowtie version 0.12.7 with the following parameter equivalents: bowtie -p <nodes> -n 2 -m 1 --best --phred33-quals
Read densities where obtained by generating a sliding window (+/-75bp) across the genome at 20bp step, using the bedmap utility from the BEDOPS suite: https://github.com/bedops/bedops
Density bigWigfiles were generated with bedGraphToBigWig (UCSC)
FDR 1% Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration for 36mer mappability
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format
|
| |
|
| Submission date |
Mar 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Audrey Letourneau |
| E-mail(s) |
audrey.letourneau@unige.ch
|
| Organization name |
University of Geneva Medical School
|
| Department |
Genetic Medicine and Development
|
| Street address |
Rue Michel-Servet 1
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE55425 |
Domains of genomewide gene expression dysregulation in Down syndrome [Dnase HS mapping] |
| GSE55426 |
Domains of genomewide gene expression dysregulation in Down syndrome |
|
| Relations |
| BioSample |
SAMN02671018 |
| SRA |
SRX480645 |
