Table 1.

Transcript and gene counts for each patient and control sample.

Sample ID	# Genes with FPKM ≥ 1	# Genes with FPKM ≥ 5	# Transcripts with FPKM ≥ 1	# Transcripts with FPKM ≥ 5
LE2C	12,111	7,648	16,734	8,152
LE4C	11,286	6,613	15,197	6,986
LE6C	11,876	7,615	16,371	8,075
DN5487	11,411	6,507	15,440	6,900
DN5511	11,601	7,000	15,972	7,565
DN76411	11,864	7,182	16,279	7,695
DN76507	11,799	7,321	16,228	7,923
KC276_2	12,265	7,843	16,971	8,457
KC366_2	11,591	7,409	15,860	7,918
KC369_2	11,761	7,768	16,240	8,258
KC388_2	11,476	7,457	15,839	8,089
KC395_2	12,442	8,240	17,242	8,738
KC400_2	11,994	7,822	16,509	8,291
KC406_2	12,948	8,462	17,887	9,057
KJ04	12,093	7,751	16,665	8,373
KJ05	11,740	7,868	16,405	8,540
KJ06	11,860	7,867	16,295	8,393
KJ09	11,784	7,563	16,437	8,119
KJ10	12,132	7,773	16,970	8,391
KJ11	11,753	7,659	16,417	8,339
KJ12	12,137	8,056	16,946	8,648
KJ13	11,859	7,972	16,519	8,566
KJ14	11,946	7,971	16,684	8,534
KJ17	11,862	7,925	16,600	8,529
KJ22	11,873	7,767	16,775	8,499
KJ25	12,094	7,925	16,758	8,547
Samples not used for differential expression analysis
DN373	12,179	7,698	16,976	8,109
DN401	11,749	7,548	16,315	8,074
DN401_2	11,743	7,587	16,337	8,132
KC276	12,342	8,010	17,102	8,583
KC366	11,727	7,608	16,063	8,075
KC369	11,861	7,932	16,394	8,428
KC388	11,722	7,974	16,173	8,637
KC395	12,491	8,310	17,306	8,842
KC400	12,076	8,012	16,711	8,507
KC406	13,025	8,559	17,950	9,155