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| Status |
Public on Aug 26, 2015 |
| Title |
CGGBP1 inhibits cytosine methylation at repetitive DNA sequences |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
By depleting CGGBP1 in normal human fibroblasts and by performing genome-wide sequencing (with and without bisulfite conversion) we show that upon CGGBP1 depletion cytosine methylation increases significantly at repeat regions. Using Pacbio sequencing of Alu and LINE-1 repeats amplified genome-wide from bisulfite converted DNA, we further establish the cytosine methylation-inhibitory functions of CGGBP1.
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| Overall design |
Control shmiR and CGGBP1 shmiR genomic DNA (both with or without sodium bisulfite conversion) used for Illumina sequencing experiments. Further bisulfite converted samples were used as templates to amplify Alu-SINEs and L1-LINEs genome wide and used for PacBio sequencing experiment.
We have sequenced the human genomic DNA (no experimental enrichment, so no modification of BAM files during analyses) and used the BAM files, the most analyzed files, to calculate the genome composition statistics, such as base composition bias etc. The differences in base composition (C->T drift upon CGGBP1-depletion) changes are our key findings.
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| Contributor(s) |
Singh U, Agarwal P |
| Citation missing |
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| Submission date |
Aug 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Umashankar Singh |
| Organization name |
IIT Gandhinagar
|
| Department |
Biological Sciences and Engineering
|
| Lab |
HoMeCell Lab
|
| Street address |
Acad Block 4 Room 317 IIT Gandhinagar Palaj
|
| City |
Gandhinagar |
| State/province |
Gujarat |
| ZIP/Postal code |
382055 |
| Country |
India |
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| Platforms (2) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
| GPL19124 |
PacBio RS (Homo sapiens) |
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| Samples (8)
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| GSM1488601 |
CGGBP1 shmiR + bisulfite converted genomic DNA |
| GSM1488602 |
Control shmiR + bisulfite converted genomic DNA |
| GSM1488603 |
CGGBP1 shmiR - genomic DNA |
| GSM1488604 |
Control shmiR - genomic DNA |
| GSM1488605 |
CGGBP1 shmiR + bisulfite converted genomic DNA+Alu PCR |
| GSM1488606 |
Control shmiR + bisulfite converted genomic DNA+Alu PCR |
| GSM1488607 |
CGGBP1 shmiR + bisulfite converted genomic DNA+LINE-1 PCR |
| GSM1488608 |
Control shmiR + bisulfite converted genomic DNA+LINE-1 PCR |
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| Relations |
| BioProject |
PRJNA259540 |
| SRA |
SRP045795 |
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