Experiment Documentation Questionnaire
[Experimental Setting]
Experimenter: Katie P
Date of experiment: 8/27/13
Project name: RWPE1 Endpoint Comparison
Experiment No. / ID:
[Sample information]
Organism: human
Strain or subtype:
Sex:
Tissue: RWPE1
[Gene / Position]
Associated gene or position description:
[Sequence Location] - IMPORTANT -
Please specify the exact genomic location of the analyzed sequence.
Accession number of sequence:
Genome browser link:
Additional position information (if applicable):
[Functional Elements]
Please specify the sequence characteristics by ticking the appropriate box(es).
( ) intergenic
( ) repetitive element, please specify type (L1, ALU, etc.):
( ) upstream (2 - 10 kb upstream of transcriptional start site)
( ) promoter (2 kb upstream to 500 bp downstream of transcription start site)
( ) exonic
( ) intronic
Does the sequence relate to a gene? Please give its official name:
[Imprinting]
Are there any allele-specific sequence polymorphisms present in sequence? Please tick.
( ) yes
( ) no
If yes, please give its position and specify the polymorphism in detail:
[Experimental details]
Which primers were used? Please give their sequences:
How was the experiment carried out? Please specify the protocol used and any deviations from it (or give a lab notebook cross-reference):
[Quality control]
Please roughly estimate the quality of your sequences:
( ) very good
( ) good
( ) average
( ) just acceptable
( ) poor
What kind of quality problems are present in the sequences? Please specify type and severity:
[Free comment (motivation / findings / problems / ...)]
Please use this space to give any additional details relating to the experiment, its motivation, or its results:
[BiQ Analyzer Documentation (automatically generated)]
Date of quality check: 27 August 2013
Conversion type: C -> T
Genomic Sequence (original): ATGAGGATGCCACTGTGGCTCAGTGATGGCGCCGAGACACAGGTGAACACTGTAAAATGTGGATGCCTGGAGGCAGCCCACACCCTGGGCCTTGGCTGGGGGAAAGGTTCCAGAAACGTCATCACAACGATGCATTTCATCAGAACTGAGCACATGAATGGGGAGGGGCAGGACTTCCTGAATGTCCCAACCCCACTGTCCCACCCTCTGTGTCAATATGAGGCTGCCTTATAAAGCACCAAGAGGCTGCCAGTGGGACATTTTCTCGGCCCTGCCAGCCCCCAGGAGGAAGGTG
Genomic Sequence (fully converted): ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAACGTTATTATAACGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTCGGTTTTGTTAGTTTTTAGGAGGAAGGTG
[BiQ Analyzer Quality Data (automatically generated)]
Number of sequences excluded during the analysis:1
Names of sequences excluded during the analysis:
03KP-S100P2R3 selection.fa - excluded in step 4 (removal of clonal sequences)
List of sequence identities relative to the genomic sequence in the final pileup (gaps ignored):
Sequence [2]: 100%
Sequence [3]: 100%
Sequence [4]: 100%
Sequence [5]: 100%
Sequence [6]: 100%
Sequence [7]: 100%
Sequence [8]: 100%
Sequence [9]: 100%
List of the sequences' conversion rates in the final pileup:
Sequence [2]: 100% (75 out of 75)
Sequence [3]: 100% (75 out of 75)
Sequence [4]: 100% (75 out of 75)
Sequence [5]: 100% (75 out of 75)
Sequence [6]: 100% (75 out of 75)
Sequence [7]: 100% (75 out of 75)
Sequence [8]: 100% (75 out of 75)
Sequence [9]: 100% (75 out of 75)
Sequence Pileup
CLUSTAL 2.1 multiple sequence alignment
Genomic_Sequence ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATAT
[2]01KP-S100P2R1selection.fa ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATAT
[3]02KP-S100P2R2selection.fa ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATAT
[4]04KP-S100P2R4selection.fa ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATAT
[5]05KP-S100P2R5selection.fa ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATAT
[6]06KP-S100P2R6selection.fa ATGAGGATGTTATTGTGGTTTAGTGATGGTGTCGAGATATAGGTGAATAT
[7]07KP-S100P2R7selection.fa ATGAGGATGTTATTGTGGTTTAGTGATGGTGTTGAGATATAGGTGAATAT
[8]08KP-S100P2R8selection.fa ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATAT
[9]10KP-S100P2R10selection.fa ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATAT
***************************** ** *****************
Genomic_Sequence TGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGG
[2]01KP-S100P2R1selection.fa TGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGG
[3]02KP-S100P2R2selection.fa TGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGG
[4]04KP-S100P2R4selection.fa TGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGG
[5]05KP-S100P2R5selection.fa TGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGG
[6]06KP-S100P2R6selection.fa TGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGG
[7]07KP-S100P2R7selection.fa TGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGG
[8]08KP-S100P2R8selection.fa TGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGG
[9]10KP-S100P2R10selection.fa TGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGG
**************************************************
Genomic_Sequence GGAAAGGTTTTAGAAACGTTATTATAACGATGTATTTTATTAGAATTGAG
[2]01KP-S100P2R1selection.fa GGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAG
[3]02KP-S100P2R2selection.fa GGAAAGGTTTTAGAAACGTTATTATAACGATGTATTTTATTAGAATTGAG
[4]04KP-S100P2R4selection.fa GGAAAGGTTTTAGAAACGTTATTATAATGATGTATTTTATTAGAATTGAG
[5]05KP-S100P2R5selection.fa GGAAAGGTTTTAGAAACGTTATTATAATGATGTATTTTATTAGAATTGAG
[6]06KP-S100P2R6selection.fa GGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAG
[7]07KP-S100P2R7selection.fa GGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAG
[8]08KP-S100P2R8selection.fa GGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAG
[9]10KP-S100P2R10selection.fa GGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAG
**************** ********** **********************
Genomic_Sequence TATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTT
[2]01KP-S100P2R1selection.fa TATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTT
[3]02KP-S100P2R2selection.fa TATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTT
[4]04KP-S100P2R4selection.fa TATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTT
[5]05KP-S100P2R5selection.fa TATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTT
[6]06KP-S100P2R6selection.fa TATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTT
[7]07KP-S100P2R7selection.fa TATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTT
[8]08KP-S100P2R8selection.fa TATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTT
[9]10KP-S100P2R10selection.fa TATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTT
**************************************************
Genomic_Sequence TTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGT
[2]01KP-S100P2R1selection.fa TTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGT
[3]02KP-S100P2R2selection.fa TTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGT
[4]04KP-S100P2R4selection.fa TTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGT
[5]05KP-S100P2R5selection.fa TTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGT
[6]06KP-S100P2R6selection.fa TTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGT
[7]07KP-S100P2R7selection.fa TTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGT
[8]08KP-S100P2R8selection.fa TTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGT
[9]10KP-S100P2R10selection.fa TTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGT
**************************************************
Genomic_Sequence TAGTGGGATATTTTTTCGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
[2]01KP-S100P2R1selection.fa TAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
[3]02KP-S100P2R2selection.fa TAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
[4]04KP-S100P2R4selection.fa TAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
[5]05KP-S100P2R5selection.fa TAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
[6]06KP-S100P2R6selection.fa TAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
[7]07KP-S100P2R7selection.fa TAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
[8]08KP-S100P2R8selection.fa TAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
[9]10KP-S100P2R10selection.fa TAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTTAGGAGGAAGGTG
**************** **************** ************
Derived Methylation Data
Genomic Sequence with numbered CpG dinucleotides:
1 2 3 4 5
ATGAGGATGCCACTGTGGCTCAGTGATGGCGCCGAGACACAGGTGAACACTGTAAAATGTGGATGCCTGGAGGCAGCCCACACCCTGGGCCTTGGCTGGGGGAAAGGTTCCAGAAACGTCATCACAACGATGCATTTCATCAGAACTGAGCACATGAATGGGGAGGGGCAGGACTTCCTGAATGTCCCAACCCCACTGTCCCACCCTCTGTGTCAATATGAGGCTGCCTTATAAAGCACCAAGAGGCTGCCAGTGGGACATTTTCTCGGCCCTGCCAGCCCCCAGGAGGAAGGTG
Methylation data for these CpG dinucleotides (1=methylated, 0=unmethylated, x=unknown):
Sequence_Identifier CpG_1 CpG_2 CpG_3 CpG_4 CpG_5
[2]01KP-S100P2R1selection.fa 1 1 0 0 0
[3]02KP-S100P2R2selection.fa 1 1 1 1 0
[4]04KP-S100P2R4selection.fa 1 1 1 0 0
[5]05KP-S100P2R5selection.fa 1 1 1 0 0
[6]06KP-S100P2R6selection.fa 0 1 0 0 0
[7]07KP-S100P2R7selection.fa 0 0 0 0 0
[8]08KP-S100P2R8selection.fa 1 1 0 0 0
[9]10KP-S100P2R10selection.fa 1 1 0 0 0
Explanation: each '1' corresponds to a methylated C, a '0' corresponds to an unmethylated C, and an 'x' corresponds to a non-CpG position.
Methylation Statistics
DNA methylation summary over all sequences
Unmethylated CpGs: 0.575 (23 cases)
Methylated CpGs: 0.425 (17 cases)
CpGs not present: 0.000 (0 cases)
CpG position statistics per column (missing values e.g. due to sequencing errors are excluded from this analysis)
Position CpG_1 CpG_2 CpG_3 CpG_4 CpG_5
Average 0.750 0.875 0.375 0.125 0.000
Std. Dev. 0.463 0.354 0.518 0.354 0.000
Sequence clone statistics per row (missing values e.g. due to sequencing errors are excluded from this analysis)
Sequence_Identifier Average Std. Dev.
[2]01KP-S100P2R1selection.fa 0.400 0.300
[3]02KP-S100P2R2selection.fa 0.800 0.200
[4]04KP-S100P2R4selection.fa 0.600 0.300
[5]05KP-S100P2R5selection.fa 0.600 0.300
[6]06KP-S100P2R6selection.fa 0.200 0.200
[7]07KP-S100P2R7selection.fa 0.000 0.000
[8]08KP-S100P2R8selection.fa 0.400 0.300
[9]10KP-S100P2R10selection.fa 0.400 0.300
Lollipop-style Representation of Methylation Data

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Explanation: Filled (black) circles correspond to methylated Cs, unfilled (white) circles correspond to unmethylated Cs, and small vertical lines without a circle correspond to missing values (e.g. caused by sequencing errors).
This image is scaled to the size of the web browser window. To zoom in please increase the window size or open the picture into an image viewer. The image resolution and other diagram parameters can be changed in BiQ Analyzer's configuration editor. Alternatively, you can copy the machine-readable results from below and paste them into the web-based diagram calculator to generate custom diagrams online.
Aggregated Representation of Methylation Data

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Explanation: Each box corresponds to one CpG position in the genomic sequence. The colored bars summarize the methylation states of all sequences at that position.
This image is scaled to the size of the web browser window. To zoom in please increase the window size or open the picture into an image viewer. The image resolution and other diagram parameters can be changed in BiQ Analyzer's configuration editor. Alternatively, you can copy the machine-readable results from below and paste them into the web-based diagram calculator to generate custom diagrams online.
Results in Machine-readable Format
>Genomic sequence: ATGAGGATGCCACTGTGGCTCAGTGATGGCGCCGAGACACAGGTGAACACTGTAAAATGTGGATGCCTGGAGGCAGCCCACACCCTGGGCCTTGGCTGGGGGAAAGGTTCCAGAAACGTCATCACAACGATGCATTTCATCAGAACTGAGCACATGAATGGGGAGGGGCAGGACTTCCTGAATGTCCCAACCCCACTGTCCCACCCTCTGTGTCAATATGAGGCTGCCTTATAAAGCACCAAGAGGCTGCCAGTGGGACATTTTCTCGGCCCTGCCAGCCCCCAGGAGGAAGGTG
[2]01KP-S100P2R1selection.fa 29 1 1 1 82 0 9 0 137 0 27
[3]02KP-S100P2R2selection.fa 29 1 1 1 82 1 9 1 137 0 27
[4]04KP-S100P2R4selection.fa 29 1 1 1 82 1 9 0 137 0 27
[5]05KP-S100P2R5selection.fa 29 1 1 1 82 1 9 0 137 0 27
[6]06KP-S100P2R6selection.fa 29 0 1 1 82 0 9 0 137 0 27
[7]07KP-S100P2R7selection.fa 29 0 1 0 82 0 9 0 137 0 27
[8]08KP-S100P2R8selection.fa 29 1 1 1 82 0 9 0 137 0 27
[9]10KP-S100P2R10selection.fa 29 1 1 1 82 0 9 0 137 0 27
Explanation: This section contains essentially the same information as the lollipop diagrams, but in a format that can be readily processed by computer programs. For example, if you need the lollipop diagram at a higher resolution or with different line breaks, then you can go to the BiQ Analyzer Diagrams website, paste the information above, and generate a new diagram without having to run through the entire quality control procedure again. The format is as follows: the first line specifies the genomic sequence and each of the following lines represents DNA methylation information for one clone (the first tab-separated value is the sequence name, the next is the distance in base pairs until the first CpG, next comes the methylation state of the first CpG, then the distance to the next CpG, and so on).
Generated with BiQ Analyzer v2.0 - (c) Christoph Bock 2008