Supplementary Information
Supplementary Figure 1. Genome-wide plot of differential expression of each gene across each mouse chromosome. Mean log2 based fold changes (tumor / normal) were plotted for each gene across the mouse genome.

Supplementary Figure 2. Aligned reads to representative differentially expressed genes.
Gene expression levels were calculated at ( a ) Ros1 and ( b ) Kras genes. The y-axis refers to read depth for each sample adjusted by the total mapped reads for that sample relative to the mean mapped reads for all samples. Sequence reads are above zero if the gene is transcribed in the sense orientation, below zero if in the antisense orientation.

Supplementary Figure 3.
Network analysis of most significantly differentially regulated genes between tumor and normal samples. ( a ) Most significantly altered biological functions based on ingenuity pathway analysis of differentially regulated genes.
( b ) Top networks associated with significantly upregulated and downregulated genes (q <
0.05) in NSCLC tumors. ( c ) Ingenuity pathway analysis connections between Kras ,

Tp53 (# sign) and the three most down-regulated genes by RNAseq analysis (marked by a
*).
Supplementary Figure 4. Parent of origin expression genome-wide. For each sample, parent-of-origin expression was determined at ~4000 single nucleotide polymorphsims, and then percent maternal expression was calculated at the mean of 5 SNP sliding windows.

Supplementary Figure 5. Cd22 variant confirmation by Sanger sequencing. The maternal allele at this position is a T and paternal allele is an A. In the tumor RNA sample, mono-allelic expression from the paternal allele is noted while genomic DNA has similar levels of expression of both paternal and maternal alleles.

Supplementary Figure 6. DNA methylation status at differentially methylated regions in the chromosome 12qF1 locus in embryonic stage tissue and lung normal and tumor tissue. Two well-studied differentially methylated regions were tested, one that is in the promoter region of Meg3 ( a ) and one that is in the intergenic region between Meg3 and
Dlk1 ( b ) and is considered to be a master regulator of imprinting of the locus.

Supplementary Figure 7.
mRNA expression profiles in FACS sorted pure tumor cells and in transplanted cells. ( a ) qPCR of Meg3 , Dlk1 and Rtl1 from FACS sorted cells positive for RFP (and activated Kras ). ( b ) Levels of the three chr12qF1 genes in cell lines from derived tumors with respect to normal lung and tumors generated after transplanting cells. (* Rtl1 probes measure both sense and antisense Rtl1 transcripts).

Supplementary Figure 8. miRNA expression profile of human lung adenocarcinoma samples from The Cancer Genome Atlas. ( a ) The percentage of microRNAs that map to the Dlk1 Dio3 locus microRNA in tumor samples (N = 346) and matched normal lung (N
= 40). Box plots are of mean with Tukey whiskers. ( b ) A scatterplot of microRNA reads per million mapped microRNAs for lung adenocarcinoma samples that contain high levels of Dlk1-Dio3 locus microRNAs (n = 34) compared with all other lung adenocarcinoma samples (N = 312). Points represent individual microRNAs, which are colored green if they align to the Dlk1-Dio3 locus and black if not.

Supplementary Table 5. List of primers for psi-check constructs.
Sh-miR-127 GATCAGCCAAGCTCAGACGGATCCGACTCCTGACCCAAGTCGGATCCGTCT
GAGCTTGGCTTTTTTGTAC
Sh-miR-134 GATCCCCCTCTGGTCAACCAGTCACACTCCTGACCCAAGTGTGACTGGTTG
ACCAGAGGGGTTTTTGTAC
Sh-miR-370 GATCACCAGGTTCCACCCCAGCAGGCCTCCTGACCCAAGGCCTGCTGGGGT
GGAACCTGGTTTTTTGTAC
Sh-miR-376c GATCACGTGAAATTTCCTCTATGTTCTCCTGACCCAAGAACATAGAGGAAA
TTTCACGTTTTTTGTAC
Sh-miR-377 GATCACAAAAGTTGCCTTTGTGTGATCTCCTGACCCAAGATCACACAAAGG
CAACTTTTGTTTTTTGTAC
Sh-miR-381 GATCACAGAGAGCTTGCCCTTGTATACTCCTGACCCAAGTATACAAGGGCA
AGCTCTCTGTTTTTTGTAC
Sh-miR-410 GATCACAGGCCATCTGTGTTATATTCTCCTGACCCAAGAATATAACACAGA
TGGCCTGTTTTTTGTAC
Sh-miR-433 GATCACACCGAGGAGCCCATCATGATCTCCTGACCCAAGATCATGATGGG
CTCCTCGGTGTTTTTTGTAC
Sh-miR-494 GATCGAGGTTTCCCGTGTATGTTTCACTCCTGACCCAAGTGAAACATACAC
GGGAAACCTCTTTTTGTAC
Sh-miR-758 GATCTAGTGGACCAGGTCACAAACTCCTGACCCAAGTTTGTGACCTGGTCC
ACTATTTTTGTAC

Supplementary Table 6. List of oligonucleotides for shRNA constructs. For each of the oligonucleotides, sequences of the sense strands are provided. The reverse complement of each sequence (minus GATC at the 5’ end and GTAC at the 3’ end) was synthesized and annealed to the sense strand.
Actr3 Forward TAGGCGATCGCTCGAGTTGATTGGGTTAGGGAGATGG
Reverse CCGCGTCGACACTAGTAAGGGTAATTCAATTTTAATTTATTGTCATC
Arfgef1 Forward TAGGCGATCGCTCGAGTGTTTTTCTGTTGGTGTTTACATTGC
Reverse CCGCGTCGACACTAGTAAATCTTTTCATGGTTTGACCTTT
Hyal1 Forward TAGGCGATCGCTCGAGGATTAGCTGCACCCAACTGC
Reverse CCGCGTCGACACTAGTATGTTAAAGCCGAATTCCGGG
Rad52 Forward TAGGCGATCGCTCGAGGGAGAGATGGCTTAGCAGTTAAC
Reverse CCGCGTCGACACTAGTGCTGGGGTTTAGCCTGCATG
Tp53i11 Forward TAGGCGATCGCTCGAGACCTGCCTGGGCCTGGACCT
Reverse CCGCGTCGACACTAGTTTGTTTCTCATTGGTTGTTTTTTGTTGTTG
Antxr1 Forward TAGGCGATCGCTCGAGAACCCAAAGTCCGAGCTCTG
Cftr
Cul1
Layn
Reverse CCGCGTCGACACTAGTTGTACAGGTTCAGCCCAGTC
Forward TAGGCGATCGCTCGAGTGCTGGGATGCTGAGGAAG
Reverse CCGCGTCGACACTAGTCTCTAAAGCTTAGTTTGCAGTTC
Forward TAGGCGATCGCTCGAGCATCTAGCAGGGTCTGCATG
Reverse CCGCGTCGACACTAGTCAATGGGAATATACACTTGCAC
Forward TAGGCGATCGCTCGAGGGAAAAACCTGGCAAGAATGC
Reverse CCGCGTCGACACTAGTGACTAACATTCTACTTCCTGC
Rtl1 Forward TAGGCGATCGCTCGAGCTCAGACCTGGCCGACGTGT
Msx2
Reverse CCGCGTCGACACTAGTTGCTCTGAAGCCTCTCTGGT
Forward TAGGCGATCGCTCGAGGAAGACCAGATGGACCAGAC
Reverse CCGCGTCGACACTAGTAGTTGGGACAGACTTTACTGC
Nsun4 Forward TAGGCGATCGCTCGAGCCACCCTGTCCCTGAAGTAG
Reverse CCGCGTCGACACTAGTCACTTTCTTGCACAGCGACTTG