characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-03-31T00:22:27Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-03-31T00:22:27Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112300330
characteristics.characteristic: External Id
characteristics.text: Cancer Research UK Cambridge Institute.
characteristics.characteristic: INSDC center name
characteristics.text: 2023-03-31T00:22:27Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-03-31T00:22:27Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14411153
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12539:e33_SII
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Mouse embryos from the appropriate somite stages (8 to 35 somites) were dissected in RNAse-free conditions in cold PBS, on silicone plates. To dissect out the somites, embryos were treated with dispase II (1mg/mL in DMEM) for 30-45 seconds at 37°C. The three most posterior pairs of somites were then collected using tungsten needles, dissecting out every somite separately. We labelled each somite pair as somite I, II or III, from the most posterior to the most anterior, respectively. Each individual somite was placed in 10µL of lysis buffer (Takara) containing RNase inhibitor. One somite from each pair was flash frozen in liquid nitrogen and stored at -80°C for later processing for RNA-seq. The matching somites were directly processed to generate ATAC-seq libraries. Individual somites were transposed with 1µL of transposome (Nextera DNA Sample Preparation kit FC-121-1030) at 37°C for 30 minutes. Samples were then purified with the Zymo Clean & Concentrator kit and eluted in 21µL of elution buffer. Transposed DNA was quantified by qPCR using 5 μl of PCR products. The number of additional cycles was determined by plotting linear Rn versus cycle and corresponded to one third of the maximum fluorescence intensity. Transposed DNA was then amplified with 13 cycles of PCR. The final products were double size-selected with AMPure beads (0.55X - 1.5X) to obtain fragments between 100bp and 700bp. Libraries were quantified and the sizes were assessed with a TapeStation machine.
characteristics.characteristic: description
characteristics.text: embryo stage
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: e33
characteristics.characteristic: individual
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: somite 35
characteristics.characteristic: organism part
characteristics.text: medial
characteristics.characteristic: sampling site
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: C57BL/6J
characteristics.characteristic: strain
characteristics.text: e33_SII
characteristics.characteristic: title