RNA labeling method

1. A method of sample analysis comprising:

a) obtaining a fragmented RNA sample comprising:

i. fragments of long RNA molecules, wherein the long RNA molecules are at least 200 nucleotides in length; and

ii. short RNA molecules of less than 200 nucleotides in length;

b) ligating an adaptor to an end of the RNA of said fragmented RNA sample to produce an adaptor-ligated sample that comprises adaptor-ligated RNA molecules comprising:

i. adaptor-ligated short RNA comprising an adaptor portion and a short RNA portion; and

ii. adaptor-ligated long RNA fragments comprising an adaptor portion and a long RNA portion;

c) hybridizing said adaptor-ligated sample to a plurality of nucleic acid probes comprising:

i. a first nucleic acid probe that comprises a nucleotide sequence that is complementary to both said adaptor portion and said short RNA portion of said adaptor-ligated short RNA; and

ii. a second probe that comprises a nucleotide sequence that is complementary to the long RNA portion of said adaptor-ligated long RNA but not said adaptor portion of said long RNA; and

d) analyzing the adaptor-ligated RNA molecules that hybridize to said probes.

2. The method of claim 1 , wherein step d) comprises measuring the abundance of a fragmented long RNA in said RNA sample and the abundance of a small RNA in said RNA sample.

3. The method of claim 1 , wherein step d) comprises releasing the adaptor-ligated RNA molecules that hybridize to said probes to produced released RNA, and sequencing the released RNA.

4. The method of claim 3 , wherein said adaptor provides a binding site for a sequencing primer.

5. The method of claim 1 , wherein said adaptor comprises a 2′ phosphate or a 2′,3′-cyclic phosphate, and said ligating is done by a eukaryotic tRNA ligase or RtcB.

6. The method of claim 1 , wherein said fragmented RNA sample is made by exposing an initial RNA sample comprising intact long RNA and short RNA to fragmentation conditions.

7. The method of claim 6 , wherein said exposing comprises contacting said initial RNA sample with a divalent cation at a temperature of at least 50° C.

8. The method of claim 6 , wherein said initial RNA sample comprises total cellular RNA from which tRNA and rRNA has been removed.

9. The method of claim 1 , wherein said short RNA molecules comprise small RNA molecules selected from the group consisting of short interfering RNA (siRNA) molecules, microRNA (miRNA) molecules, tiny non-coding RNA (tncRNA) molecules or small modulatory RNA (smRNA) molecules.

10. The method of claim 1 , wherein said long RNA molecules comprise lincRNA molecules or mRNA molecules.

11. The method of claim 1 , wherein said adaptor is in the range of 6 to 12nucleotides in length.

12. The method of claim 1 , further comprising treating said fragmented RNA sample with a polynucleotide kinase or a phosphatase in the absence of ATP prior to said ligating step b), to produce ligatable RNA that lacks a 5′ phosphate in said fragmented RNA sample.

13. The method of claim 1 , wherein the RNA of said fragmented RNA sample is labeled prior to or after said ligating step b).

14. The method of claim 1 , wherein said adaptor is a labeled adaptor.

15. The method of claim 1 , wherein step c) comprises hybridizing said adaptor-ligated sample to an array comprising a plurality of nucleic acid probes.

16. The method of claim 1 , wherein said method comprises ligating an adaptor to the 5′ end of the RNA of said fragmented RNA sample.

17. The method of claim 12 , wherein said method comprises ligating an adaptor to the 3′ end of the RNA of said fragmented RNA sample.