|
| Status |
Public on Jul 20, 2011 |
| Title |
Hela Dnase I hypersensitivity |
| Sample type |
SRA |
| |
|
| Source name |
Hela
|
| Organism |
Homo sapiens |
| Characteristics |
subcellular: Whole cell
cell type: Hela
|
| Treatment protocol |
DNase footprinting was done as previously described (Hesselberth et al., 2009).
|
| Growth protocol |
Hela cells were cultured as described previously (http://genome.ucsc.edu/ENCODE/protocols/cell/human/HeLa-S3_protocol.pdf)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were firstly size fractionated by sucrose gradient centrifugation to obtain fragments that were cleaved on both ends by DNase I, referred to as DNase I double-hit fragments, as previously described (Sabo et al. ,2006). Resultant fragments of 100-500 bp in length were then used to construct DNaseI libraries according to Illumina's genomic prep kit protocol with minor modifications as previously described (Hesselberth et al., 2009). Libraries were sequenced to produce 36 bp reads according to standard sequencing-by-synthesis methodology on an Illumina Genome Analyzer (GAII).
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Dnase I cleaved DNA fragments
|
| Data processing |
Sequence data were evaluated and aligned to the reference mitochondrial genome using BowTie (Langmead et al., 2009) using default parameters and returning only unique aligning read. The 5â termini of the sequenced reads, corresponding to the cleavage sites, was used to assign each nucleotide within the mitochondrial genome an integer score corresponding to DNase I cleavage frequency. The subsequent DNase I cleavage profiles were subject to de-spiking to account for DNase I dinucleotide cleavage bias was corrected in cleavage frequencies as previously described (Hesselberth et al., 2009).
|
| |
|
| Submission date |
Jul 19, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim R. Mercer |
| Organization name |
Garvan
|
| Lab |
Prof. John Mattick
|
| Street address |
384 Victoria Street Darlinghurst NSW 2010
|
| City |
Sydney |
| State/province |
New South Wales |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE30772 |
The human mitochondrial transcriptome |
|
| Relations |
| SRA |
SRX084350 |
| BioSample |
SAMN00672479 |
