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
131KP-Nes1B1selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
234KP-Nes1B4selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT--AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTT-GCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
338KP-Nes1B8selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT--AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGCTCGTAGCCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
432KP-Nes1B2selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
539KP-Nes1B9selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGTGTTTAGTTTGGAGTTGTTGTAGTTT
640KP-Nes1B10selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGCGTTTTAAGAGGTTTTCGCGTTTAATTTGGAG------------
733KP-Nes1B3selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTNATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
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 [%] 85.7 85.7 85.7 71.4 71.4 85.7 71.4


CG site No.

85.7%85.7%85.7%71.4%71.4%85.7%71.4%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 20.4% (10 cases)
Methylated CpGs: 79.6% (39 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (49 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
31KP-Nes1B1selection 100.0
34KP-Nes1B4selection 100.0
38KP-Nes1B8selection 100.0
32KP-Nes1B2selection 85.7
39KP-Nes1B9selection 85.7
40KP-Nes1B10selection 85.7
33KP-Nes1B3selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/4/13
Project name RWPE1 Endpoint Comparison
Tissue B26
Gene or position Nes #1