Text+version+of+summary+for+searching+2-7-13

Random Hexamer cDNA Library Sequence Summary 2-7-13

Control Liver Library Summary

Name (clone) size (bp) BLAST match Query Coverage E-value Max Identity Database L1 none L2 229 Mouse DNA sequence from clone RP23-391P24 on chromosome 2, complete sequence 99% 2.00E-111 99% nr nt L3 Plasmid vector pFKm4, complete sequence L4 Plasmid vector pFKm4, complete sequence L5 Mus musculus papillary renal cell carcinoma (translocation-associated) (Prcc), mRNA L6 none L7 Plasmid vector pFKm4, complete sequence L8 none L9 none L10 Plasmid vector pFKm4, complete sequence

How many sequences were mostly all As with a very short sequence after the As? "5/10"

How many sequences did not sequence well and are therefore likely poly A sequences (the plasmid vector pFKm4 sequences)? "4/10"

How many sequences matched a mouse sequence? "1/10"

Tumor Library Summary

Name (clone) size BLAST match Query Coverage E-value Max Identity Database T1 23 none T2 23 none T3 103 Mus musculus BAC clone RP24-463C3 from 3, complete sequence 96% 2.00E-47 100% nr nt T4 23 none T5 23 none T6 157 Mus musculus interferon regulatory factor 2 binding protein 2 (Irf2bp2), mRNA 96% 2.00E-75 100% mouse RefSeq RNA T7 23 T8 23 T9 416 Mus musculus lysosomal-associated protein transmembrane 5 (Laptm5), mRNA 99% 0 100% mouse RefSeq RNA T10 23

short poly A sequences "7/10"

mouse sequences "3/10"

Position of Sequences Relative to Transcript

Only two sequences from the tumor library align with mouse RNAseq transcript sequences. The other mouse sequences align with genomic sequences, but not known RNA sequences. These RNAseq sequences do not just align to the 3’ end which is one of the aspects I was trying to avoid when we decided to make the random hexamer library so this is good.

Tumor Library Sequence 6

Tumor Library Sequence 9