|
| Status |
Public on Jan 30, 2012 |
| Title |
DNAse-Seq |
| Sample type |
SRA |
| |
|
| Source name |
erythroid cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: erythroid cells
strain: C57BL/6
|
| Treatment protocol |
DNAse I hypersensititivity digestion was performed on mouse primary erythroid cells were obtained from the spleens of acetylphenylhydrazine-treated mice (Spivak et al., 1973; Vernimmen et al., 2009).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei from 5x107 mature primary erythroid cells, obtained from the spleen of a phenylhydrazine-treated adult mice as described (Spivak et al., 1973), were digested with increasing concentrations (10, 20, 40, 80U) of DnaseI (Roche 10776785001) and DNA was extracted by phenol/chloroform (Higgs et al., 1990). Since, as a general rule, the DHSs are not all equally intense and more than one concentration of DnaseI is required to detect them, 1.5 mg of DNA from each of digestion (10, 20, 40, 80U) was pooled and blunt-ended with T4 DNA Polymerase (NEB), and prepared for Illumina-Solexa sequencing following the manufacture's protocol. The DnaseI -digested material was amplified using PCR primer PE1.0 and PE2.0 for 10 cycles. A short extension time (15 seconds) was used to allow amplification of only the short fragments generated by the DnaseI digestion. Finally, the 200-500 bp window library was gel purified.
Model- GAIIx Chemistry-SBS v4 cBot single generation kit with v4 flow cell SCS 2.8 RTA 1.8 Recipe v7.4
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The reads were aligned to the mm9 mouse genome build using bowtie (version 0.12.3) with indices on m2 (map twice to the genome). Before downstream analysis duplicate reads of the same chromosome and start position were collapsed to a single representative read to exclude overrepresented PCR products. All aligned reads starts were summed in sliding windows of 300 bp to create summary windows.
|
| |
|
| Submission date |
Mar 12, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Monika S Kowalczyk |
| E-mail(s) |
monika.kowalczyk@imm.ox.ac.uk
|
| URL |
http://www.imm.ox.ac.uk/wimm-research/molhaem/doug-higgs
|
| Organization name |
Weatherall Institute of Molecular Medicine, University of Oxford
|
| Department |
MRC Molecular Haematology Unit
|
| Lab |
Higgs Group
|
| Street address |
Headley Way
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE27919 |
Genome-wide map of DNaseI hypersensitivity in mouse erythroid cells. |
| GSE27921 |
Intragenic enhancers act as alternative promoters |
|
| Relations |
| BioSample |
SAMN02196931 |
