RNA sequencing of chicken limb distal mesenchyme cells to compare gene expression over time and in heterochronic grafted cells

Distal limb mesenchyme cells were collected from embryonic chickens at Hamburger Hamilton (HH) stages HH24, HH27, and HH29, and also from samples that had been grafted from HH27 to HH20 and left to develop for 24 hours (equivalent to HH24). Samples were collected in triplicate (with 10 distal tips pooled per replicate), the RNA extracted, and sequenced on a HiSeq 2000 (Instrument: ST300). Bioinformatic and clustering analyses were performed to determine whether grafted cells are more similar to HH29 or HH24 samples, ie. which genes can be reset to expression levels observed in an earlier developmental stage.