Protocols used in RNA Extraction
================================

Long Cytoplasmic RNA A+ and A-:  Long Cytoplasmic RNA was isolated using
Qiagens RNeasy Protocol.  Qiagens Qligotex kit was used to separate
Poly-A(+) from Poly-A(-).

Long Nuclear RNA A+ and A-: Cell were lysed with Qiagens RLN buffer and the
nuclei were spun out, resuspended in Qiagen's RLT buffer, layered over a
Cesium Chloride bed and spun at 24,000 rpm for a minimum of 20 hours. The
pellet was recovered and cleaned up on Qiagens RNeasy kit. Qiagens Qligotex
kit was used to separate Poly-A(+) from Poly-A(-).

Long Polysomal RNA A+ and A-: Cyclohexamide arrested cell lysate were
layered on a 20-60% sucrose gradient and spun at 27,000 rpm for 4 hours.
The fractions and analyzed by UV-spectroscopy using a programmable Density
Gradient Fractionation System Foxy Jr. (Isco).

Long Nucleoplasm, Nucleoli and Chromatin: We used the protocol found in
Bhorjee and Pederson (1973). 

Small Cytoplasmic RNA: Small Cytoplasmic RNA was isolated using Qiagens
RNA/DNA kit.

Small Nuclear RNA:  Small Nuclear RNA was isolated using Qiagens RNA/DNA
kit.


References
==========

Bhorjee JS, Pederson T. Chromatin: its isolation from cultured mammalian
cells with particular reference to contamination by nuclear ribnucleoprotein
particles. Biochemistry. 1973 Jul 3;12(14):2766-73.

Kapranov, P. et.al. RNA maps
reveal new RNA classes and a possible function for pervasive transcription.
Science. 2007 Jun 8;316(5830):1484-8.