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4dn:phase1:working_groups:omics_data_standards:minutes-06-13-2016
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4dn:phase1:working_groups:omics_data_standards:minutes-06-13-2016 [2019/02/14 15:49] rcalandrelli created |
4dn:phase1:working_groups:omics_data_standards:minutes-06-13-2016 [2025/04/22 16:21] (current) |
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| ===== Experiment Procedures, meta-data ===== | ===== Experiment Procedures, meta-data ===== | ||
| - | * | + | * Finalizing the experiment protocol. Derive the Hi-C standard from existing, published in situ Hi-C protocols. Determine what is variable and what should be unified and precise documentation of such variables |
| - | + | * Digestion time for DNAs may vary, depending on the exact type of DNAs (e.g. mitochondrial vs genomic). | |
| - | Finalizing the experiment protocol. Derive the Hi-C standard from existing, published in situ Hi-C protocols\\ Determine what is variable and what should be unified and precise documentation of such variables | + | * in-situ is a fairly standard protocol that different labs are using. Two variations were brought up as being worthwhile improvements: |
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| - | Digestion time for DNAs may vary, depending on the exact type of DNAs (e.g. mitochondrial vs genomic). | + | |
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| - | in-situ is a fairly standard protocol that different labs are using. Two variations were brought up as being worthwhile improvements: | + | |
| * Job Dekker: Dangling sequence removal is an important step that should be added to the standard protocol to improve library quality. | * Job Dekker: Dangling sequence removal is an important step that should be added to the standard protocol to improve library quality. | ||
| * ?: For temperature during overhang filling, 23C is better than 37 C (enzyme dependent?) | * ?: For temperature during overhang filling, 23C is better than 37 C (enzyme dependent?) | ||
| - | * | + | * Other similar procedures that may need a different protocol. May put different categories (like the narrow and broad for ChIP-seq in ENCODE) and may be based on Hi-C protocol before |
| - | + | * Micro-C procedure | |
| - | Other similar procedures that may need a different protocol\\ May put different categories (like the narrow and broad for ChIP-seq in ENCODE) and may be based on Hi-C protocol before | + | * DNase Hi-C (a different protocol from the ones with restriction enzymes) |
| - | + | * How will the protocol be encoded in the meta-data structure? | |
| - | * | + | * Trade-off between tracking information in searchable fields vs. ease of logging. |
| - | + | * Follow ENCODE's example: standard protocols are provided as pdf, variations become meta-data fields. | |
| - | Micro-C procedure | + | * Medata for ENCODE ChIP-seq: |
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| - | DNase Hi-C (a different protocol from the ones with restriction enzymes) | + | |
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| - | How will the protocol be encoded in the meta-data structure? | + | |
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| - | Trade-off between tracking information in searchable fields vs. ease of logging. | + | |
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| - | Follow ENCODE's example: standard protocols are provided as pdf, variations become meta-data fields. | + | |
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| - | Medata for ENCODE ChIP-seq: | + | |
| * Biosample: description of cell, condition, treatment. We may need to expand to describe genome editing. | * Biosample: description of cell, condition, treatment. We may need to expand to describe genome editing. | ||
| * Antibody: We will not need. | * Antibody: We will not need. | ||
| * Protocol: fragmentation method, fragment length. handful others(?) | * Protocol: fragmentation method, fragment length. handful others(?) | ||
| * For Hi-C, we will need to add a field for restriction enzyme (information about crosslinking time, temperature etc, may be in pdf or have separate fields, probably pdf is fine.) | * For Hi-C, we will need to add a field for restriction enzyme (information about crosslinking time, temperature etc, may be in pdf or have separate fields, probably pdf is fine.) | ||
| - | * | + | * Do we need to keep metadata for Hi-C QC prior to sequencing. |
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| - | Do we need to keep metadata for Hi-C QC prior to sequencing. | + | |
| * e.g. like antibody validation in ENCODE | * e.g. like antibody validation in ENCODE | ||
| * We can't think of examples for Hi-C that need to be reported. | * We can't think of examples for Hi-C that need to be reported. | ||
| * Assume data prep passed basic wetlab QC in the prep stages. (there are natural checkpoints, go/no-go. All data submitted to DCIC is go/go/go. | * Assume data prep passed basic wetlab QC in the prep stages. (there are natural checkpoints, go/no-go. All data submitted to DCIC is go/go/go. | ||
| - | * | + | * computational QC data (e.g. read depth, PCR duplicate proportion, reproducibility, intra/inter) |
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| - | computational QC data (e.g. read depth, PCR duplicate proportion, reproducibility, intra/inter) | + | |
| * can be determined after data is taken in by DCIC. | * can be determined after data is taken in by DCIC. | ||
| - | * | + | * Cross consortium data sharing/merging with ENCODE |
| - | + | * DCIC: this will naturally be easy since we are starting with their metadata and database model. | |
| - | Cross consortium data sharing/merging with ENCODE | + | |
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| - | DCIC: this will naturally be easy since we are starting with their metadata and database model. | + | |
| ===== Data formats ===== | ===== Data formats ===== | ||
4dn/phase1/working_groups/omics_data_standards/minutes-06-13-2016.1550188186.txt.gz · Last modified: 2025/04/22 16:21 (external edit)