 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 23, 2022 |
| Title |
Anchor-Based Bisulfite Sequencing determines genome-wide DNA methylation |
| Organisms |
Escherichia coli; Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling; however, WGBS is costly as it requires sequencing coverage over the entire genome. Here we introduce Anchor-Based Bisulfite Sequencing (ABBS). We show that ABBS captures accurate DNA methylation information in Escherichia coli and mammalian cells, while requiring approximately 20 times fewer sequencing reads than WGBS. The ABBS protocol is simple and can be performed in a single day.
|
| |
|
| Overall design |
WGBS and ABBS on E. coli and K562 cells
|
| |
|
| Contributor(s) |
Delatte B |
| Citation(s) |
35710818 |
| Submission date |
Jul 25, 2021 |
| Last update date |
Jun 17, 2022 |
| Contact name |
Benjamin Delatte |
| E-mail(s) |
benche65@gmail.com
|
| Organization name |
Active Motif
|
| Department |
Advanced Research
|
| Street address |
1914 Palomar Oaks Way STE 150
|
| City |
Carlsbad |
| State/province |
CA |
| ZIP/Postal code |
92008 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
|
| Samples (15)
|
| GSM5471115 |
E. coli, K12 strain, clone 1, untreated, WGBS primer |
| GSM5471116 |
E. coli, K12 strain, clone 1, untreated, ABBS primer |
| GSM5471117 |
E. coli, K12 strain, clone 1, bisulfited, WGBS primer |
| GSM5471118 |
E. coli, K12 strain, clone 1, bisulfited, ABBS primer |
| GSM5471119 |
E. coli, K12 strain, clone 2, untreated, WGBS primer |
| GSM5471120 |
E. coli, K12 strain, clone 2, untreated, ABBS primer |
| GSM5471121 |
E. coli, K12 strain, clone 2, bisulfited, WGBS primer |
| GSM5471122 |
E. coli, K12 strain, clone 2, bisulfited, ABBS primer |
| GSM5471123 |
E. coli, K12 strain, clone 1, bisulfited, ABBS primer (A.M. library prep) |
| GSM5471124 |
E. coli, K12 strain, clone 2, bisulfited, ABBS primer (A.M. library prep) |
| GSM5471125 |
K562, WGBS experiment |
| GSM5471126 |
K562, ABBS experiment |
| GSM5471127 |
K562, ABBS experiment (A.M. library prep) |
| GSM5747763 |
E. coli, B strain, untreated, WGBS primer |
| GSM5747764 |
E. coli, B strain, untreated, ABBS primer |
|
| Relations |
| BioProject |
PRJNA749583 |
| SRA |
SRP329794 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE180796_RAW.tar |
14.8 Gb |
(http)(custom) |
TAR (of BEDGRAPH, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...