characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2015-01-19T17:03:06Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T17:21:12Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2452100
characteristics.characteristic: External Id
characteristics.text: European Molecular Biology Laboratory, Developmental Biology Unit
characteristics.characteristic: INSDC center name
characteristics.text: 2015-01-19T17:03:06Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T17:21:12Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS433528
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2488:ap2c-wtLFB-GCTA
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: ap2c-wtLFB-GCTA (wild type)
characteristics.characteristic: chromosomal aberration
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: The whole embryos, latral and medial parts of forebrains, and heart were taken from E11.5d embryos. The limbs were taken from E12.5d embryos. The cells from the forebrains and the heart were dissociated by pipetting gently and passed through the Falcon Cell Strainers with 70um pore. Then they were fixed in 12 ml of 2% PFA/PBS at the room temperature for 10 min. 1.5 ml of 1 M glycine was added to quench the PFA. The cells were washed once in PBS and then frozen in Liquid nitrogen and stored at -80 degrees C. They were then incubated in 1 ml of the lysis buffer (50 mM Tris (pH7.5), 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, 1x complete proteinase inhibitors (Roche)) at 4 degrees C for 10 minutes. For the limbs and the whole embryo, instead, the single cell nuclei were prepared passing the fixed and lysed cells through needles for several times. After treating the nuclei in 0.3% SDS for 1 hour, followed by an additional 1 hour incubation with 2.5% Triton X-100, we digested the fixed genomic DNA with NlaIII enzyme at 37 degrees C for overnight. After the NlaIII was heat-inactivated, we ligated the DNA with T4 DNA ligase at 16 degrees C for overnight. Then the DNA was reverse cross-linked and purified through phenol-chloroform extraction and ethanol precipitation. The ligated DNA was then subjected to digestion by the second enzyme (DpnII) and ligation. After the ethanol precipitation, the eluted DNA was further purified twice with QIAquick PCR Purification Kit (QIAGEN). The concentration of the DNA was measured by NanoDrop. The inverse PCR was performed using 3.2ug of the libraries as templates except for the one from INV-M whole embryo, for which we used 1.8ug to obtain the 4C library.The reading primers had 3-6 nucleotides of tag sequence between the Illumina read adaptor and the annealing sequence, so that we could demultiplex the libraries after sequencing them together. The PCR products were purified with the High Pure PCR Product Purification Kit (Roche), and subsequently with QIAquick PCR Purification Kit (QIAGEN).
characteristics.characteristic: description
characteristics.text: embrynoic day 11.5
characteristics.characteristic: developmental stage
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: lateral forebrain
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0001890
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: fresh specimen
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000971
characteristics.characteristic: specimen with known storage state
characteristics.text: 129/Ola
characteristics.characteristic: strain
characteristics.text: ap2c-wtLFB-GCTA
characteristics.characteristic: title