Table 1. Validation of DO-RIP-seq cDNA libraries prior to deep sequencing.
cDNA sequences in fasta format from HuR DO-RIP experiments were inserted into pGEM-T vectors, used to transform E. coli, and colonies were picked for Sanger sequencing. Sequences are from experiments with optimal MNase digestion conditions and over-digestion conditions. Note that over-digestion conditions yielded mostly rRNA fragments, while optimal conditions produce mostly mRNA fragments.
|
HuR DO-RIP sequences from optimal digestion conditions
|
| >CCT8_CDS_chr21:30,434,842-30,435,033_- |
| TTAGTGAGGCTAAACTCAAAATGGGATCTCCGAAGACTTTGTAA |
| >HSPA5_CDS_chr9:128,000,571-128,000,591_- |
| ACAGGTGACCTGGTACTGCTT |
| >PAIP1_CDS_chr5:43,535,713-43,535,744_- |
| AAAGTTGACAGGATCAGTTTTGGAAGATGCTTGG |
| >SON_CDS_chr21:34,929,588-34,929,612_+ |
| AGTCAGGAGGAGCTACTATAGAAGA |
| >LPGAT1_3UTR_chr1:211919329-211919357_- |
| TTGTTTTCTTTGTTCTTTTTTTGAAGTCA |
| >RAN_3UTR_chr12:131,360,755-131,360,795_+ |
| ATCTTGTTTGTTACTGTCATTCCCATTCCTTTTCGTTTAGA |
| >SS18_3UTR_chr18:23597210-23597238_- |
| TATGTTTTTCCCTTTTTTATGTTGGTTGA |
| >SUB1_3UTR_chr5:32,602,122-32,602,167_+ |
| ATTAAGCTTTACTGTTATAGTAGGTAATATGGTTAGTTTGTAGGGA |
| >DNAJB11_intron_chr3:186,296,085-186,296,130_+ |
| TTTTTGTTTCTTCCAGTTTTATTCAATTCCAAACAGCGCTTTTATG |
| >NCOA7_intron_chr6:126,209,995-126,210,024_+ |
| AGTTTCCGTTTTGTTTTTTGCCTTTCCTCC |
| >chrM:14,678-14,726 |
| ACAACGATGGTTTTTCATATCATTGGTCGTGGTTGTAGTCCGTGCGAGA |
| >PPP6R3_5UTR_chr11:68,287,053-68,287,076_+ |
| ACCTGTAATGGGCAAGGAGCCACA |
| >DNAJC14_anti-sense_chr12:56,216,465-56,216,505_+ |
| ACACTCAGCACAGTATCTGGCACTCTTAGGTTCCCGGTCCA |
|
HuR DO-RIP sequences from over-digested conditions |
| >rRNA_chrUn_gl000220:115,785-115,844_- |
| GCAACGGAGGCCATCGCCCGTCCCTTCGGAACGGCGCTCGCCCATCTCTCAGGACCGACT |
| >rRNA_chr17:33,478,208-33,478,234_- |
| ATATTAGTCAGCGGAGGAAAAGAAACT |
| >rRNA_chr21:9,827,183-9,827,220_- |
| GCACGCATCCCCCCCGCGAAGGGGGTCAGCGCCCGTCG |
| >rRNA_chrUn_gl000220:110,738-110,773_- |
| GTACAAAGGGCAGGGACTTAATCAACGCAAGCTTAT |
| >rRNA_chr12:20,704,449-20,704,484_- |
| AATTCCGATAACGAACGAGACTCTGGCATGCTAACT |
| >rRNA_chrUn_gl000220:109,717-109,755_- |
| AATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGT |
| >rRNA_chr17:33,478,235-33,478,275_- |
| CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGC |
| >7SK_chr6:52,860,434-52,860,469_- |
| CCCTGGCGATCAATGGGGTGACAGATGTCGCAGCCA |
| >rRNA_chrUn_gl000220:110,523-110,559_- |
| GCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCT |