Experiment Documentation Questionnaire

Experiment Documentation Questionnaire

[Experimental Setting]

Experimenter: Anja Fagin

Date of experiment: 11.07.2007

Project name: TSLC1 II, Köln

Experiment No. / ID: 01/15800/1/1

[Sample information]

Organism: Homo Sapiens

Strain or subtype:

Sex:

Tissue: Neuroblastoma

[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 GO 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 where used? Please give their sequences:

TSLC1: gtgagtgatggaaatttgtaatgtttggtt (311) atgttattagtattttattagttg (456)

Sequencing with M13 forw primer, Seqlab. Sequencing reactions from 25.04.06 and 06.07.07

[Quality control]

Please roughly estimate the quality of your sequences:

( ) very good

( ) good

(x) average

( ) just acceptable

( ) poor

What kind of quality problems are present in the sequences? Please specify type and degree:

Break down of the sequence because of T repeats

[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: 12 Juli 2007

Conversion type: C -> T

Genomic Sequence (original): GTGAGTGACGGAAATTTGCAACGTCTGGTTCGCTAGGCCAGATGCACTCGGTGTGCGGGACAGAGGACCCTCTTAAGGGAGATTCTCCAGTCGTCGGTNTGATACAGCGATTGCTATAAACATT

Genomic Sequence (fully converted): GTGAGTGACGGAAATTTGTAACGTTTGGTTCGTTAGGTTAGATGTATTCGGTGTGCGGGATAGAGGATTTTTTTAAGGGAGATTTTTTAGTCGTCGGTNTGATATAGCGATTGTTATAAATATT

[BiQ Analyzer Quality Data (automatically generated)]

No sequences were excluded during the analysis.

List of the sequence identities relative to the genomic sequence in the final pileup (gaps ignored):

Sequence [2]: 99%

Sequence [3]: 99%

Sequence [4]: 99%

Sequence [5]: 99%

Sequence [6]: 99%

Sequence [7]: 99%

List of the sequences' conversion rates in the final pileup:

Sequence [2]: 100% (18 out of 18)

Sequence [3]: 100% (18 out of 18)

Sequence [4]: 100% (18 out of 18)

Sequence [5]: 100% (18 out of 18)

Sequence [6]: 100% (18 out of 18)

Sequence [7]: 89% (16 out of 18)

ClustalW Sequence Pileup

CLUSTAL W (1.83) multiple sequence alignment

Genomic_Sequence ------

[2]12.1b.seq --TTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCT

[3]12.4b.seq AATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCT

[4]12.5.seq AATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCT

[5]12.6b.seq AATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCT

[6]12.7.seq --TTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCT

[7]F12_2.seq ------ATACGACTCA-CTATAGGGCGAATTGGGCC--CTC

Genomic_Sequence ------GT

[2]12.1b.seq TGGTACCGAGCTCGGAT--CCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGCCCTTGT

[3]12.4b.seq TGGTACCGAGCTCGGAT--CCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGCCCTTGT

[4]12.5.seq TGGTACCGAGCTCGGAT--CCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGCCCTTGT

[5]12.6b.seq TGGTACCGAGCTCGGAT--CCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGCCCTTGT

[6]12.7.seq TGGTACCGAGCTCGGAT--CCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGCCCTTGT

[7]F12_2.seq TAGATGCATGCTCGAGCGGCCGCCAGTG-TGATGGATA-TCTGC-AGAATTCGCCCTTGT

**

Genomic_Sequence GAGTGACGGAAATTTGTAACGTTTGGTTCGTTAGGTTAGATGTATTCGGTGTGCGGGATA

[2]12.1b.seq GAGTGACGGAAATTTGTAATGTTTGGTTTGTTAGGTTAGATGTATTTGGTGTGTGGGATA

[3]12.4b.seq GAGTGACGGAAATTTGTAATGTTTGGTTTGTTAGGTTAGATGTATTTGGTGTGTGGGATA

[4]12.5.seq GAGTGACGGAAATTTGTAATGTTTGGTTTGTTAGGTTAGATGTATTTGGTGTGTGGGATA

[5]12.6b.seq GAGTGACGGAAATTTGTAATGTTTGGTTTGTTAGGTTAGATGTATTTGGTGTGTGGGATA

[6]12.7.seq GAGTGACGGAAATTTGTAATGTTTGGTTTGTTAGGTTAGATGTATTTGGTGTGTGGGATA

[7]F12_2.seq GAGTGACGGAAATTTGTAATGTTTGGTTTGTTAGGTTAGATGCATTTGGTGTGTGGGATA

******************* ******** ************* *** ****** ******

Genomic_Sequence GAGGATTTTTTTAAGGGAGATTTTTTAGTCGTCGGTNTGATATAGCGATTGTTATAAATA

[2]12.1b.seq GAGGATTTTTTTAAGGGAGATTTTTTAGTTGTTGGTTTGATATAGTGATTGTTATAAATA

[3]12.4b.seq GAGGATTTTTTTAAGGGAGATTTTTTAGTTGTTGGTTTGATATAGTGATTGTTATAAATA

[4]12.5.seq GAGGATTTTTTTAAGGGAGATTTTTTAGTTGTTGGTTTGATATAGTGATTGTTATAAATA

[5]12.6b.seq GAGGATTTTTTTAAGGGAGATTTTTTAGTTGTTGGTTTGATATAGTGATTGTTATAAATA

[6]12.7.seq GAGGATTTTTTTAAGGGAGATTTTTTAGTTGTTGGTTTGATATAGTGATTGTTATAAATA

[7]F12_2.seq GAGGATTTTTTTAAGGGAGATTTTTTAGTTGTTGGTTTGATATAGTGATTGTTATAAACA

***************************** ** *** ******** ************ *

Genomic_Sequence TT------

[2]12.1b.seq TTTTTAATAAAGGTGTATAAGAAGTTAGATTAAGGGCGAATTCTGCAGAT--ATCCATCA

[3]12.4b.seq TTTTTAATAAAGGTGTATAAGAAGTTAGATTAAGGGCGAATTCTGCAGAT--ATCCATCA

[4]12.5.seq TTTTTAATAAAGGTGTATAAGAAGTTAGATTAAGGGCGAATTCTGCAGAT--ATCCATCA

[5]12.6b.seq TTTTTAATAAAGGTGTATAAGAAGTTAGATTAAGGGCGAATTCTGCAGAT--ATCCATCA

[6]12.7.seq TTTTTAATAAAGGTGTATAAGAAGTTAGATTAAGGGCGAATTCTGCAGAT--ATCCATCA

[7]F12_2.seq TTTTTAATAAAGGTGTATAAGAAGTTAGGTT-----TGTTTTTTGGAGTTTGAGTTTTTG

**

Genomic_Sequence ------

[2]12.1b.seq CACTGGCGGCCGCTCGAGCATGCATCTAGAGGGCCCAATTCGCCCTATAGTGAGTCGNN

[3]12.4b.seq CACTGGCGGCCGCTCGAGCATGCATCTAGAGGGCCCAATTCGCCCTATAGTGAGTNN--

[4]12.5.seq CACTGGCGGCCGCTCGAGCATGCATCTAGAGGGCCCAATTCGCCCTATAGTGAGTNN--

[5]12.6b.seq CACTGGCGGCCGCTCGAGCATGCATCTAGAGGGCCCAATTCGCCCTATAGTGAGTNN--

[6]12.7.seq CACTGGCGGCCGCTCGAGCATGCATCTAGAGGGCCCAATTCGCCCTATAGTGAGTCNN-

[7]F12_2.seq TAC-GTTAGGTGTTTGGGANAATATTTTTNNNNNNNNNNNNNNNNNNNNNN------

Derived Methylation Data

Genomic Sequence with numbered CpG dinucleotides:

1 2 3 4 5

GTGAGTGACGGAAATTTGCAACGTCTGGTTCGCTAGGCCAGATGCACTCGGTGTGCGGGACAGAGGACCCTCTTA

6 7 8 AGGGAGATTCTCCAGTCGTCGGTNTGATACAGCGATTGCTATAAACATT

Methylation data for these CpG dinucleotides (1=methylated, 0=unmethylated, x=unknown):

Sequence_IdentifierCpG_1CpG_2CpG_3CpG_4CpG_5CpG_6CpG_7CpG_8

[2]12.1b.seq 10000000

[3]12.4b.seq 10000000

[4]12.5.seq 10000000

[5]12.6b.seq 10000000

[6]12.7.seq 10000000

[7]F12_2.seq 10000000

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:0,875% (42 cases)

Methylated CpGs: 0,125% (6 cases)

CpGs not present: 0,000% (0 cases)

Per column / CpG position statistics (for each position, sequences where the CpG is missing are excluded from this analysis)

Position CpG_1CpG_2CpG_3CpG_4CpG_5CpG_6CpG_7CpG_8

Average 1,0000,0000,0000,0000,0000,0000,0000,000

Std. Dev.0,0000,0000,0000,0000,0000,0000,0000,000

Per row / sequence clone statistics (positions where the CpG is missing are excluded from this analysis)

Sequence_IdentifierAverageStd. Dev.

[2]12.1b.seq 0,1250,109

[3]12.4b.seq 0,1250,109

[4]12.5.seq 0,1250,109

[5]12.6b.seq 0,1250,109

[6]12.7.seq 0,1250,109

[7]F12_2.seq 0,1250,109

Results in Machine-readable Format

>Genomic sequence: GTGAGTGACGGAAATTTGCAACGTCTGGTTCGCTAGGCCAGATGCACTCGGTGTGCGGGACAGAGGACCCTCTTAAGGGAGATTCTCCAGTCGTCGGTNTGATACAGCGATTGCTATAAACATT

[2]12.1b.seq8111070160503401011 0 15

[3]12.4b.seq8111070160503401011 0 15

[4]12.5.seq8111070160503401011 0 15

[5]12.6b.seq8111070160503401011 0 15

[6]12.7.seq8111070160503401011 0 15

[7]F12_2.seq8111070160503401011 0 15

Explanation: This section contains essentially the same information as lollipop diagrams, but in a format that can be readily processed by computer programs. For example, if you need a 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).

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