|
| Status |
Public on Jun 29, 2011 |
| Title |
HepG2_FAIRE_REP2 |
| Sample type |
SRA |
| |
|
| Source name |
liver carcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: liver carcinoma cells
|
| Growth protocol |
Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
FAIRE was performed as described (Giresi et al. 2007; Giresi and Lieb 2009) DNA fragments are prepped for sequencing using the recommended protocol except that samples are amplified prior to gel extraction. Amplified DNA between 150 and 300 bp are excised from the gel, recovered using Qiagen Gel Extraction kit, and sequenced.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
FAIRE-seq
|
| Data processing |
Sequences from each experiment were aligned to the genome using Maq (Li et al., 2008) and those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes). The resulting digital signal was converted to a continuous wiggle track using F-Seq (http://www.genome.duke.edu/labs/furey/software/fseq/) that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Discrete sites (peaks) were identified from DNase-seq using by setting a F-Seq score cutoff based on fitting these data to a gamma distribution and determining the threshold at a p-value of 0.1.
|
| |
|
| Submission date |
Jun 27, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Terry Furey |
| E-mail(s) |
terry.furey@unc.edu
|
| Organization name |
UNC-Chapel Hill
|
| Department |
Genetics
|
| Lab |
Furey
|
| Street address |
5022 Genetic Medicine Building, CB#7264
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE30225 |
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [FAIRE_seq] |
| GSE30227 |
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity |
|
| Relations |
| SRA |
SRX080119 |
| BioSample |
SAMN00631168 |
