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| Status |
Public on Feb 13, 2014 |
| Title |
HL1_DNaseSeq |
| Sample type |
SRA |
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| Source name |
Lymphoblastoid cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Lymphoblastoid
biopsy site: blood, peripheral vein
coriell catalog #: AG16408
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| Biomaterial provider |
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=AG16408
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| Growth protocol |
We obtained two cell types from Coriell Cell Repositories for this study: skin fibroblast cells and lymphoblastoid cell lines (LCLs). Primary skin fibroblast cells from three human, three chimpanzee, and three macaque individuals. LCLs, which are B cells immortalized with Epstein-Barr Virus, were obtained from the same three human and three chimpanzee individuals that fibroblasts were isolated from. EBV does not reliably transfect macaque lymphocyte cells, so matched macaque LCLs cells were not available for this study. Importantly, other recent genome-wide studies that used macaque LCLs were of B-Lymphocyte cells transformed with rhesus herpes papio virus, a close relative of human EBV. Cells from all species were grown in standard growth media. Fibroblast growth media consisted of Gibco's MEM (10370-021), L-Glutamine (25030-081), Pen/Strep (15140-122), and 10% FBS (Hyclone SH30070). LCLs growth media consisted of Gibco's RPMI (21870) media with L-Glutamine, Pen/Strep, and 15% FBS. We harvested ~35 million cells for DNase analysis.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Primary fibroblast and lymphoblastoid (LCLs) cell were grown in culture then pelleted before immediately proceeding to DNase-seq library preparations. All DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106). Briefly, cells were lysed and incubated at 37¡C for various times (5 min to 1 hour) and optimal DNase digestion was confirmed by pulsed field gel electrophoresis (Song L and Crawford GE. Cold Spring Harbor protocols 2010(2):pdb prot5384).
DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106).
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Illumina CASAVA 1.3 software used for single-end basecalling.
Sequenced reads were trimmed to the first 20bp to remove adaptor sequence using custom scripts, and masked for low-complexity or low-quality sequence, then mapped to the samples native whole genome (hg19 for human, panTro2 for chimpanzee and rheMac2 for macaque) using BWA version 0.6.1-r104 with default indexing (index -a bwtsw) and aln parameters (aln -t 8) to create alignment SAI files.
SAM files were created from the SAI files using bwa samse with default parameters, then filtered for alignments with greater than 4 mismatches using custom scripts.
The SAM files (after filtering for mismatches >4) were converted to BAM format using "samtools view", then sorted via chromosome using "samtools sort", then converted to BED format using "bedtools bamtobed".
Sharp sequence pileups introduced by PCR amplification artifacts or potential misalignments were filtered out to reflect a maximum acceptable read count for a peaks region based on a Poisson distribution.
Each 20-mer alignment of chimpanzee and macaque species were converted to a human genome coordinate using LiftOver (Hinrichs AS, et al. 2006. Nucleic Acids Res 34: D590–598) using a minMatch setting of 0.80.
Custom scripts were used to pull out the exact bp positions that were cut by DNaseI (ExactCuts.bigWig in hg19 space for all species).
Genome_build: hg19, panTro2, rheMac2
Supplementary_files_format_and_content: bigWig format (hg19)
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| Submission date |
Feb 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoichiro Shibata |
| E-mail(s) |
yoichiro.shibata@gmail.com
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| Organization name |
Duke University
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| Department |
Inst. of Genome Sciences and Policy
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| Lab |
Greg Crawford
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| Street address |
101 Science Dr
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platform ID |
GPL10999 |
| Series (2) |
| GSE54907 |
Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection [Dnase-seq] |
| GSE54908 |
Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection |
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| Relations |
| BioSample |
SAMN02640536 |
| SRA |
SRX469951 |
| Named Annotation |
GSM1326422_HL1_ExactCuts.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1326422_HL1_ExactCuts.bigWig |
776.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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