Experiment summary for ENCSR123UVP
doi:10.17989/ENCSR123UVP
Summary
- Status
- released
- Assay
- HiC (in situ Hi-C)
- Biosample summary
- Homo sapiens HCT116 genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, (insertion) using CRISPR targeting H. sapiens RAD21
- Biosample Type
- cell line
- Replication type
- isogenic
- Description
- in situ MboI Hi-C
- Nucleic acid type
- DNA
- Library starting quantity
- 5000000cells [1-1]5000000cells [1-3]5000000cells [2-4]5000000cells [2-1]2800000cells [3-1]2800000cells [4-1]5000000cells [1-2]5000000cells [2-2]2800000cells [3-2]5000000cells [2-3]2800000cells [4-2]2800000cells [4-3]
- Size range
- 300-500
- Fragmentation methods
- chemical (MboI restriction)
- Size selection method
- SPRI beads
- Platform
- Illumina HiSeq X Ten
Attribution
ENCODE4 project
- Lab
- Erez Aiden, Baylor
- Award
- UM1HG009375 (Erez Aiden, Baylor)
- Project
- ENCODE
- External resources
- Aliases
- erez-aiden:HCT-116-RAD21-mAC-no-auxin
- Date submitted
- June 1, 2020
- Date released
- August 5, 2020
- Submitter comment
- This dataset is missing genome subcompartments, nuclease cleavage frequency, and pairs due to being run on the earlier version 1.2.1 of the pipeline which uses juicer tools version 2.13.05. This dataset runs out of memory on the create_hic step of the current pipeline 1.15.1 which uses juicer tools version 2.13.06 and cannot be successfully processed.
Isogenic replicates
Isogenic replicate | Technical replicate | Summary | Biosample | Modifications | Library |
|---|---|---|---|---|---|
| 1 | 1 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS996WTD | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB105ZCM |
| 1 | 3 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS996WTD | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB227YQE |
| 2 | 4 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS245OAR | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB097YAV |
| 2 | 1 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS245OAR | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB464TUE |
| 3 | 1 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS661LPA | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB063TYY |
| 4 | 1 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS010BHG | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB849BDC |
| 1 | 2 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS996WTD | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB428BCX |
| 2 | 2 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS245OAR | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB481NOX |
| 3 | 2 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS661LPA | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB593IHL |
| 2 | 3 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS245OAR | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB838TZH |
| 4 | 2 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS010BHG | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB349TJE |
| 4 | 3 | Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 | ENCBS010BHG | ENCGM785YNS, ENCGM489TXA, ENCGM561PJN | ENCLB948GZG |