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| Status |
Public on Apr 08, 2020 |
| Title |
Exonuclease combinations reduce noises in 3D genomics technologies |
| Organism |
Mus musculus |
| Experiment type |
Other
Third-party reanalysis
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| Summary |
Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased valid-pairs ratio from 30-40% to 70-80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency.
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| Overall design |
For dilution system, LIC-Hi-C treatments mean the noises of Hi-C were removed by “Lambda and Exonuclease I” exonuclease combination for 1h, which has three replicates (LIC-Hi-C-1,LIC-Hi-C-2,LIC-Hi-C-3). LRC-Hi-C-1, which means the noises of Hi-C were removed by “Lambda and RecJF” exonuclease combination for 1h.LRC-Hi-C 2-4(three replicates), which means the noises of Hi-C were removed by “Lambda and RecJF” exonuclease combination for 1 min. The formers are belong to Exo-Hi-C. Hi-C 1-3 (three replicates) are Exo-Hi-C control without exonuclease combination treatment. GSM862721(Standard Hi-C 1),GSM1718027(Standard Hi-C 2) and GSM862720(Standard Hi-C 3) are also set as control groups.We have downloaded these three data.We re-analyzed and named them as Standard Hi-C 1, Standard Hi-C 2 and Standard Hi-C 3 in our papers. For in situ system, IIIIC-in situ Hi-C 4-6 (three replicates) and 10-12 (another three replicates) treatments mean in situ Hi-C in this study were treated by “Exonuclease I and Exonuclease III” exonuclease combination for 1 min. LIC-in situ Hi-C 4-6 (three replicates) and 10-11 (another two replicates) treatments mean in situ Hi-C in this study were treated by “Lambda and Exonuclease I” exonuclease combination for 1 min. The formers are belong to In situ exo-Hi-C.In situ Hi-C 1-3 (three replicates) and 12-14 (another three replicates) are in situ exo-Hi-C control without exonuclease combination treatment (named as in situ Hi-C). HIC088,HIC094,HIC096 are also set as control groups.We have downloaded these three data.We re-analyzed and named them as Rao et al. insitu Hi-C in our papers.
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| Contributor(s) |
Kong S, Li Q, Zhang G, Li Q, Huang Q, Huang L, Zhang H, Huang Y, Peng Y, Qin B, Zhang Y |
| Citation(s) |
32128590 |
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| Submission date |
Jan 25, 2019 |
| Last update date |
Apr 10, 2020 |
| Contact name |
Qing Li |
| E-mail(s) |
[email protected]
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| Organization name |
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences,
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| Street address |
No 7,Pengfei Road,Dapeng District
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| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
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| Platforms (2) |
| GPL21273 |
HiSeq X Ten (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (27)
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| Relations |
| Reanalysis of |
GSM862721 |
| Reanalysis of |
GSM1718027 |
| Reanalysis of |
GSM862720 |
| BioProject |
PRJNA517112 |
| SRA |
SRP182047 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE125656_GSM1718027_HiCUP_summary_report.txt.gz |
634 b |
(ftp)(http) |
TXT |
| GSE125656_GSM1718027_allValidPairs.txt.gz |
867.4 Mb |
(ftp)(http) |
TXT |
| GSE125656_GSM862720.mRSstat.txt.gz |
204 b |
(ftp)(http) |
TXT |
| GSE125656_GSM862720_allValidPairs.mergestat.txt.gz |
211 b |
(ftp)(http) |
TXT |
| GSE125656_GSM862721.mRSstat.txt.gz |
203 b |
(ftp)(http) |
TXT |
| GSE125656_GSM862721_allValidPairs.hic |
1.2 Gb |
(ftp)(http) |
HIC |
| GSE125656_GSM862721_allValidPairs.mergestat.txt.gz |
170 b |
(ftp)(http) |
TXT |
| GSE125656_RAW.tar |
16.7 Gb |
(http)(custom) |
TAR (of HIC, TXT) |
| GSE125656_SRR1658716_allValidPairs.txt.gz |
703.6 Mb |
(ftp)(http) |
TXT |
| GSE125656_SRR1658722_allValidPairs.txt.gz |
838.9 Mb |
(ftp)(http) |
TXT |
| GSE125656_SRR1658724_allValidPairs.txt.gz |
1.1 Gb |
(ftp)(http) |
TXT |
| GSE125656_SRX116341_allValidPairs.txt.gz |
2.5 Gb |
(ftp)(http) |
TXT |
| GSE125656_SRX116342_allValidPairs.txt.gz |
1.5 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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