In layman terms, what is going on in the following procedure? This is taken from

Question

In layman terms, what is going on in the following procedure? This is taken from the methods section of an article that is studying the differences between moles and mice in regards to their digging specialization brought about by Hox genes.

In situ hybridization

A digoxigenin-labeled antisense RNA probe used on both T. occidentalis and M. musculus embryos was synthesized from a plasmid containing a PCR product of the coding sequence of HoxA9 from the mouse (GenBank accession number: NM_010456.2), using cDNA retrotranscribed from embryonic mouse mRNA as a PCR template. Mouse RNA probes of HoxD9 (NM_013555; Zappavigna et al. 1991), HoxD11 (X71422; Gerard et al. 1993), and HoxD13 (NM_008275; Dolle et al. 1991) were generously provided by Denis Duboule, Switzerland, and used on both mole and mouse embryos. Whole-mount in situ hybridization was performed according to a standard protocol (Bickelmann et al. 2012). As a distinct cartilage primordium with perichondrium in the humerus of T. occidentalis is present at 11.5 dpc (days post coitum) and ossification starts at 13.5 dpc, we examined embryos as early as 9.5–13.5 dpc (corresponding to stages illustrated by Bickelmann et al. 2014, Fig. 2, A–C). Throughout its entire development, the humerus straddles the boundary between the limb and the body wall with its proximal half being embedded in the latter (Fig. 1G).

Explanation / Answer

Insitu hybridization require RNA probes (here tagged with digoxigenin). When these probes are allowed to i cubate with your tissue/organ sample, they go and bind to its complementary RNA molecule. This helps one to know about its spatio-temporal expression.

3 probes (for God D9, HoxD11, HoxD13) were obtained ready made.

HoxA9 had to be made. So they isolated mouse RNA. Used HoxA9 specific primers to PCR amplify it. They cloned this amplified product into a plasmid. It was allowed to transcribe and the obtained RNA was digoxigenin -tagged.

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