Bead Gallery® stone beads of choice: http://www.halcraft.com/products/bead-gallery/
Silk that will pass through bead holes (#8 High Performance is great for most)
Beadalon® Knot-a-Bead
Scissors
Jeweler's cement
Optional: chain; French Wire to fit silk

Knot-a-Bead Instructions: http://www.beadalon.com/images/Knot_A_BEAD_Instructions.pdf

To make a continuous knotted gemstone strand: Pass the cord through the first three beads, leave an inch and tie then follow the Knot-a-Bead instructions to tie the first knot. Once the rest of the beads are knotted, position the first few un-knotted beads close to the knotted beads leaving enough space to add two more knots. Pass the needle through the first bead and tie a knot by hand, then pass through the second bead and tie a knot by hand. Pass through the third bead (which should already be knotted). Add a drop of glue inside the bead before and let it dry before cutting off any extra cording.

To make a knotted gemstone strand that's connected to chain: Pass the cord through a bead and about 1/4” of French Wire. Pass through the chain and back into the first bead so the French Wire protects the silk and forms a loop through the chain. Tie the first knot by hand, then pass through another bead and follow the instructions for the Knot-a-Bead. Use the same technique at the end.