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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 09:37]
oh created 		4dn:phase1:working_groups:omics_data_standards:minutes-11-14-2016 [2025/04/22 16:21] (current)
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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 
-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: +      - 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. 
- +      - Biotin removal step will affect yield and should be kept optional instead of mandatory. The SOP will be without biotin removal (all published in situ Hi-C data have no such step). 
-      - +      - 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. 
-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. +        - 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. 
-      - +      - 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. 
-Biotin removal step will affect yield and should be kept optional instead of mandatory. The SOP will be without biotin removal (all published in situ Hi-C data have no such step). +      - 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 
- +  - Other data types 
-All variations from the base protocol (SOP) should be recorded in the meta data so that DCIC can work on those. +  - Joint WG of OMICS and Images. Maybe incorporate a larger group than the current OMICS WG to include some members from the imaging WG.
- +
-      - +
- +
-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. +
- +
-      - +
- +
-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. +
- +
-      - +
- +
-Sequencing Depth: required 500M raw paired-end sequence reads now in the final document. +
- +
-      - +
- +
-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 +
- +
-  - +
- +
-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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4dn/phase1/working_groups/omics_data_standards/minutes-11-14-2016.1550252241.txt.gz · Last modified: 2025/04/22 16:21 (external edit)

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