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| Status |
Public on May 10, 2017 |
| Title |
CTCF.sample1.bound |
| Sample type |
SRA |
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| Source name |
In vitro protein-DNA binding reactions
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| Organism |
Mus musculus |
| Characteristics |
dna library composition: Including unmethylated dsDNA library CTCF-R1-R5, and M.sssI methylated dsDNA library CTCF-R1-R5-M.sssI
recombinant protein used: mouse CTCF (Finger 1 to Finger 9)
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| Treatment protocol |
All EMSA reactions were done in 9% Tris-glycine gel, 200V, 30mins
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After EMSA, DNA fragments were cut and extracted by gel extraction buffer at 50C for 30mins.
For each portion of DNA fragment, PE1 and PE2 PCR primers were used to PCR amplify extracted DNA by at least 8 cycles (95C 15s, 52C 15s, 72C 30s)
For each particular sample, there are two raw data files, i.e., bound reads and unbound reads with different Illumina Index. The processed data file was based on analysis of Bound and Unbound data together.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
CTCF_sample1_processed
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| Data processing |
Library strategy: Methyl-Spec-seq
Methylation property identification: For any particular DNA variant inside library, it carries particular barcode to indicate its methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated. Thus acording to the unique methylation barcode information, each read was identified and sorted to its methylation type.
Variant reads counting and sorting: For each randomized binding site, its number in Bound and Unbound portions were counted separately. The Bound/Unbound ratio was supposedly porportional to its relative binding affinity, and the negative logarithm of this ratio indicates the relative binding energy in kT unit.
Energy logo visualization: Based on the binding energy for particular reference and all its single variants, an energy logo can be generated to indicate the specificity of particular protein-DNA interactions. Futhermore, besides conventional G-T-A-C bases, we used two extra “M" and ”W" to represent methylated cytosine on upper and lower strand of DNA respectively, in which the height of M or W indicate the extra binding energy contribution between methylated and unmethylated base.
Supplementary_files_format_and_content: All processed data were saved in .excel files, including the methylation property, bound reads, unbound reads, Bound/Unbound ratio, relative binding energy for each variant.
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| Submission date |
May 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zheng Zuo |
| E-mail(s) |
zeropin@live.cn
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| Organization name |
Stanford university
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| Department |
Genetics
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| Street address |
Stanford
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| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94040 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE98542 |
Methyl-Spec-seq control data sets |
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| Relations |
| BioSample |
SAMN06890681 |
| SRA |
SRX2783742 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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