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4dn:phase1:working_groups:omics_data_standards:minutes-11-14-2016
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4dn:phase1:working_groups:omics_data_standards:minutes-11-14-2016 [2019/02/15 09:44] oh |
4dn:phase1:working_groups:omics_data_standards:minutes-11-14-2016 [2025/04/22 16:21] (current) |
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| |~~TABLE_CELL_WRAP_START~~<WRAP> | |~~TABLE_CELL_WRAP_START~~<WRAP> | ||
| - | - | + | - Standard guidelines. Consist of experimental part and protocols, agreed on using the in situ Hi-C paper as a standard. Minor variations on the experimental protocols. This document may be updated on an annual basis and will be kept stable in the meantime. Concerns: |
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| - | Standard guidelines\\ Consist of experimental part and protocols, agreed on using the in situ Hi-C paper as a standard\\ MInor variations on the experimental protocols\\ This document may be updated on an annual basis and will be kept stable in the meantime.\\ Concerns: | + | |
| - Which other enzymes can be used? Hind III give very good quality data | - Which other enzymes can be used? Hind III give very good quality data | ||
| - and are more reproducible but may have lower resolution than 4-base cutters. The current wording allows individual PIs to choose their restriction enzyme based on their current situation. | - and are more reproducible but may have lower resolution than 4-base cutters. The current wording allows individual PIs to choose their restriction enzyme based on their current situation. | ||
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| - All variations from the base protocol (SOP) should be recorded in the meta data so that DCIC can work on those. | - All variations from the base protocol (SOP) should be recorded in the meta data so that DCIC can work on those. | ||
| - Cell density at the time of harvest: Is the cell density need to be standardized? \__Suspension cells will be in per unit volume and adherent cells will be in per unit area. | - Cell density at the time of harvest: Is the cell density need to be standardized? \__Suspension cells will be in per unit volume and adherent cells will be in per unit area. | ||
| - | - Although this appears out of scope - it need to be included in experimental / cell-line WG SOP so that researchers will record it before actually generating data (and submitting them), it might still be OK to include in this data standard document. | + | - Although this appears out of scope - it need to be included in experimental / cell-line WG SOP so that researchers will record it before actually generating data (and submitting them), it might still be OK to include in this data standard document. |
| - Indicating whether there are other frozen aliquots and point to them in meta data so that people know which datasets are coming from the same biological replicate. | - Indicating whether there are other frozen aliquots and point to them in meta data so that people know which datasets are coming from the same biological replicate. | ||
| - Crosslinking: standardized in SOP and have no dramatic differences among groups. | - Crosslinking: standardized in SOP and have no dramatic differences among groups. | ||
| - Sequencing Depth: required 500M raw paired-end sequence reads now in the final document. | - Sequencing Depth: required 500M raw paired-end sequence reads now in the final document. | ||
| - Earlier experiments may use variations. | - Earlier experiments may use variations. | ||
| - | - | + | - Format for pairs file. Standardized file format for read pairs (developed by Burak), text-based file before chromosomal binning. Planned to be approved during next meeting: . |
| - | + | - ChIA-PET. Defer to the next meeting | |
| - | Format for pairs file\\ Standardized file format for read pairs (developed by Burak), text-based file before chromosomal binning\\ Planned to be approved during next meeting: . | + | - Other data types |
| - | + | - Joint WG of OMICS and Images. Maybe incorporate a larger group than the current OMICS WG to include some members from the imaging WG. | |
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| - | ChIA-PET\\ Defer to the next meeting | + | |
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| - | - | + | |
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| - | Other data types | + | |
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| - | Joint WG of OMICS and Images\\ Maybe incorporate a larger group than the current OMICS WG to include some members from the imaging WG.\\ \__ | + | |
| + | \\ \__ | ||
| </WRAP>~~TABLE_CELL_WRAP_STOP~~| | </WRAP>~~TABLE_CELL_WRAP_STOP~~| | ||
4dn/phase1/working_groups/omics_data_standards/minutes-11-14-2016.1550252647.txt.gz · Last modified: 2025/04/22 16:21 (external edit)