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| Status |
Public on Feb 17, 2012 |
| Title |
zebrafish adult liver cells DnaseI |
| Sample type |
SRA |
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| Source name |
adult liver cells
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| Organism |
Danio rerio |
| Characteristics |
tissue: adult liver cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Zebrafish peripheral blood was collected by cardiac puncture in anesthetized adult zebrafish. As the mature erythrocytes in lower vertebrates retain their nuclei, we are able to isolate erythrocyte nuclei from peripheral blood. DNase I hypersensitivity assays were arried out. Briefly, red blood cells were treated with 0.025% Igepal in Buffer A (15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM Spermidine) for 8 minutes. The released nuclei were pelleted and incubated for 3 minutes at 37C in DNase buffer (13.5mM Tris-Cl pH8.0, 88.5 mM NaCl, 54 mM KCl, 0.9 mM EDTA, 0.45 mM EGTA, 0.45 mM Spermidine, 6 mM CaCl2) plus 0, 40, 60, 80 or120 units/ml of DNaseI (Sigma Aldrich). The reaction was stopped by the addition of an equivalent volume of Stop Buffer (50mM Tris-Cl pH 8.0, 100 mM NaCl, 0.10 %SDS, 100 mM EDTA) and incubated for 1 hr with 1100 units/ml Proteinase K. Small DNase I fragments from the 120 unit DNaseI treatement were enriched using a sucrose gradient. These ends were then labeled and amplified for Solexa sequencing
Small genomic DNA fragments resulted from DNase I treatment of intact nuclei were enriched using a sucrose gradient centrifugation after optimal DNase I treatment of isolated nuclei
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
DNaseI in zebrafish adult liver cells
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| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using "bowtie -p 8 --mm -n 3 -v 3 -k 2 --phred33-quals". BAM files were created by combining FASTQ files using samtools merge function.
For all samples, aligned sequences were processed with MACS (Zhang et al., 2008) software with command line input parameters: gsize = 15000000000; bandwidth = 50; and p-value = 1e-09.
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| Submission date |
Feb 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Anthony Dominc DiBiase |
| E-mail(s) |
adibiase@enders.tch.harvard.edu
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| Organization name |
Children's Hospital Boston
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| Department |
Hem/Onc
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| Lab |
Zon Lab
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| Street address |
KFRB, 1 Blackfan St, Suite 8216
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL9319 |
| Series (2) |
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| Relations |
| SRA |
SRX120322 |
| BioSample |
SAMN00790967 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM876971_dnaseI_liver-DS8510_danrer7.wig.gz |
75.2 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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