BISMA results:

Reference sequence (original) : ACCAGGTTTCTGAGAACTGGCTCCTGATTCAGCAGCCAGCTAGCCCCACTCCCTTCCCAGAAGGTCTCTGAGCTTCATAAGGGACTTTCTGGAGCTTTCTGGGACTTTCTCTCACCCAGGCCCTCAACCTCCTCACCTGGAACTTTTCAGTAGCCCGCAGCCGCTCCTGCCAGCGGCCCTCCAACCTCTGTTCCAACGCTGCCCTGCGCTCCAGGAGGCCTCCGCGCTCAGCCTGGAGCTGCTGCAGCTC
Reference sequence (converted): ATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
Number CpG in Reference sequence: 7

Parameters used:

Alignment mode: pairwise alignment of reference sequence and experimental sequences
Lower threshold conversion rate: 95%
Lower threshold sequence identity: 90%
Upper threshold of N-sites at cytosine positions: 20%
Upper threshold insertions/deletions: 20%

Final sequence alignment of the sequences included:

                                                                                                                                                                                                                                                              
                                                                                                    1                   1                   1                   1                   1                   2                   2                   2             
                   2                   4                    6                   8                   0                   2                   4                   6                   8                   0                   2                   4             
Number Sequence_id                    0                   0                    0                   0                   0                   0                   0                   0                   0                   0                   0                   0             
Reference ATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
128KP-Nes1A8selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTCTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
223KP-Nes1A3selectionATTAGGTTTT-GAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGTGTTTAGTTTGGAGTTGTTGTAGTTT
324KP-Nes1A4selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAGTTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGTGTTTAGTTTGGAGTTGTTGTAGTTT
422KP-Nes1A2selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
525KP-Nes1A5selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
626KP-Nes1A6selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
727KP-Nes1A7selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
830KP-Nes1A10selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTCAACGTTGTTTTGCGTTTTAGGAGGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
921KP-Nes1A1selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT--AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTNGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
1029KP-Nes1A9selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTTGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
Legend: methylated CpG position unmethylated CpG position unconverted cytosine cytosine at unexpected position

Methylation pattern in subclones:

methylated  , unmethylated  , unknown 

Methylation status of CpG-sites cytosine in the sequence context


Methylation pattern



Average methylation for each CpG site:

CpG site 1 2 3 4 5 6 7
CpG position 156 162 174 197 207 223 225
Methylation [%] 100.0 77.8 90.0 50.0 50.0 90.0 70.0


CG site No.

100.0%77.8%90.0%50.0%50.0%90.0%70.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 24.6% (17 cases)
Methylated CpGs: 75.4% (52 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 98.6% (69 cases)
CpGs not analyzed: 1.4% (1 case)


Average methylation for each clone:

Seq. identifier Average 
28KP-Nes1A8selection 100.0
23KP-Nes1A3selection 85.7
24KP-Nes1A4selection 85.7
22KP-Nes1A2selection 71.4
25KP-Nes1A5selection 71.4
26KP-Nes1A6selection 71.4
27KP-Nes1A7selection 71.4
30KP-Nes1A10selection 71.4
21KP-Nes1A1selection 66.7
29KP-Nes1A9selection 57.1



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/4/13
Project name RWPE1 Endpoint Comparison
Tissue CAsE-PE
Gene or position Nes #1