title: GSM1153956: Mouse_Proximal_limb_Hoxa4; Mus musculus; OTHER
library_construction_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/).
attributes.tag: GEO Accession
attributes.value: GSM1153956