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Sample GSM748516 Query DataSets for GSM748516
Status Public on Jun 29, 2011
Title HelaS3_FAIRE_REP2
Sample type SRA
 
Source name cervical carcinoma
Organism Homo sapiens
Characteristics cell line: HelaS3
cell type: cervical carcinoma
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 3’ 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 SRX080117
BioSample SAMN00631166

Supplementary file Size Download File type/resource
GSM748516_HelaS3_UNCFAIRESeq_align_rep2.bed.gz 536.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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