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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jan 21, 2014 |
Title |
Zebrafish_Hoxa11a |
Sample type |
SRA |
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Source name |
Whole embryo 5dpf
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Organism |
Danio rerio |
Characteristics |
strain: TU tissue: Whole embryo age: 5 dpf genotype: wild type
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Extracted molecule |
genomic DNA |
Extraction protocol |
4C–seq libraries were constructed as described before (Noordermeer et al. 2011). Mouse libraries consisted of 52 dissected E12.5 proximal forelimb buds, distal forelimb buds or forebrains. Zebrafish libraries consisted of approximately 300 5 dpf embryos from the TU strain. For mouse viewpoints, the primary restriction enzyme used was NlaIII (New England Biolabs, R0125L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543M). For zebrafish viewpoints, the primary restriction enzyme was DpnII (New England Biolabs, R0543M) and the secondary enzyme was TaqαI (New England Biolabs, R0149M) (using the latter enzyme DNA was cut for 8 hours at 65°C). For each viewpoint between 1.3 and 2.6 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences. Multiplexed samples were sequenced on the Illumina HiSeq system using 100 bp single-end reads according to the manufacturer’s specifications. 4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline of the BBCF HTSstation (available at http://htsstation.epfl.ch and discussed in (Noordermeer et al. 2011)). Mouse samples were mapped to the ENSEMBL Mouse assembly NCBIM37 (mm9) and zebrafish samples were mapped to the ENSEMBL Zebrafish assembly Zv9. 4C PCR was sequenced with Illumina Genome AnalyzerHiSeq 2000. Data was mapped to the mouse genome using HTSstation (http://htsstation.vital-it.ch/).
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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Description |
library strategy: 4C-Seq
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Data processing |
Reads were mapped to the mm9 (NCBIM37) Mouse genome assembly, to the Zf9 Zebrafish genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7). De-multiplexing, mapping and 4C-analysis were performed through HTSstation (http://htsstation.epfl.ch) according to previously described procedure (Noordermeer et al., 2011). Figures were made using a running mean algorithm using a window size of eleven fragments. 4C tracks were normalized to the same total intensity over the regions visualuzed in the figures, such as to see only changes in contacts distribution and to minimize PCR complexity bias in each samples. . Both the mapping and the 4C-seq analysis were done through HTSstation (http://htsstation.epfl.ch/). Genome_build: mouse: MGSCv37 Genome_build: zebrafish: Zv9 Supplementary_files_format_and_content: density files (bedGraph) and smoothed/normalized data (bedGraph), one per viewpoint, per tissue
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Submission date |
Jun 05, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Marion LELEU |
Organization name |
EPFL
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Department |
School of Life Sciences
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Lab |
Laboratory of developmental genomics
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Street address |
EPFL-SV-ISREC-UPDUB- Station 19
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City |
Lausanne |
ZIP/Postal code |
1015 |
Country |
Switzerland |
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Platform ID |
GPL14875 |
Series (1) |
GSE47644 |
Conservation and divergence of regulatory strategies and the origin of tetrapod digits |
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Relations |
BioSample |
SAMN02191226 |
SRA |
SRX293719 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1153975_Woltering_Zebrafish_Hoxa11a_frags_regs.bedGraph.gz |
6.9 Kb |
(ftp)(http) |
BEDGRAPH |
GSM1153975_Woltering_Zebrafish_Hoxa11a_smoothed11.bedGraph.gz |
12.5 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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