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Sample GSM1153980 Query DataSets for GSM1153980
Status Public on Jan 21, 2014
Title Zebrafish_Hoxa2b
Sample type SRA
 
Source name Whole embryo 5dpf
Organism Danio rerio
Characteristics strain: TU
tissue: Whole embryo
age: 5 dpf
genotype: wild type
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/).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description library strategy: 4C-Seq
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
 
Submission date Jun 05, 2013
Last update date May 15, 2019
Contact name Marion LELEU
Organization name EPFL
Department School of Life Sciences
Lab Laboratory of developmental genomics
Street address EPFL-SV-ISREC-UPDUB- Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platform ID GPL14875
Series (1)
GSE47644 Conservation and divergence of regulatory strategies and the origin of tetrapod digits
Relations
BioSample SAMN02191231
SRA SRX293724

Supplementary file Size Download File type/resource
GSM1153980_Woltering_Zebrafish_Hoxa2b_frags_regs.bedGraph.gz 3.7 Kb (ftp)(http) BEDGRAPH
GSM1153980_Woltering_Zebrafish_Hoxa2b_smoothed11.bedGraph.gz 5.2 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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