|
| Status |
Public on Nov 08, 2013 |
| Title |
HTE-B2 |
| Sample type |
SRA |
| |
|
| Source name |
Human tracheal epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: adult
tissue: trachea
cell type: epithelia
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Growth conditions as described in Davis PB, Silski CL, Kercsmar CM, et al. Beta-adrenergic receptors on human tracheal epithelial cells in primary culture. Am J Physiol 1990;258:C71–6.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction was performed according to the protocol at http://genome.ucsc.edu/ENCODE/protocols/general/Duke_DNase_protocol.pdf
Library Construction was performed according to the protocol at http://genome.ucsc.edu/ENCODE/protocols/general/Duke_DNase_protocol.pdf
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
DNase-seq data biological replicate 2
|
| Data processing |
Data processing is described in detail at http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=346639599&c=chr21&g=wgEncodeOpenChromDnase and is briefly summarized below.
Sequences from each experiment were aligned to the genome using BWA (Li et al., 2008) for the GRCh37 (hg19) assembly. The command used for these alignments was: > bwa aln -t 8 genome.fa s_1.sequence.txt.bfq > s_1.sequence.txt.sai where genome.fa is the whole genome sequence and s_1.sequence.txt.bfq is one lane of sequences converted into the required bfq format.
Using F-seq, the resulting digital signal was converted to a continuous wiggle track that employs a Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Input data was generated for several cell lines. These were used directly to create a control/background model used for F-Seq when generating signal annotations for these cell lines. These models were meant to correct for sequencing biases, alignment artifacts, and copy number changes in these cell lines. Input data was not generated directly for other cell lines. For cell lines for which there is no input experiment available, the peaks were generated using the control of generic_male or generic_female, as an attempt to create a general background based on input data from several cell types. These files are in "iff" format, which is used when calling peaks with F-seq software, and can be downloaded from the production lab directly from under the section titled "Copy number / karyotype correction." Using a general background model derived from the available Input data sets provided corrections for sequencing biases and alignment artifacts, but did not correct for cell type-specific copy number changes. The exact command used for this step was: > fseq -l 600 -v -f 0 -b <bff files> -p <iff files> aligments.bed where the bff files are the background files based on alignability, the iff files are the background files based on the Input experiments, and alignments.bed is a bed file of filtered sequence alignments.
Discrete DNaseI HS sites (peaks) were identified from DNase-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: TE_finalPeaks.npf contains the combined peak calls for HTE B1 and B2.
|
| |
|
| Submission date |
Nov 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ann Harris |
| Organization name |
Lurie Children's Hospital of Chicago Research Center
|
| Street address |
2430 N Halsted Street Box 211
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60614 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE52179 |
A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function (DNase-hypersensitivity) |
| GSE52181 |
A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function |
|
| Relations |
| BioSample |
SAMN02400202 |
| SRA |
SRX374730 |
