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--- 4dn:phase1:working_groups:omics_data_standards:minutes-02-25-2019 [2019/03/25 13:05]
xiaoyi_cao created
+++ 4dn:phase1:working_groups:omics_data_standards:minutes-02-25-2019 [2025/04/22 16:21] (current)
@@ Line 1: / Line 1: @@
+Agenda -
+  - Schedule for future presentations
+      - March 25: PLAC-seq/HiChIP standard presentation by Miao Yu
+      - May 27th: GAM standard presentation by Ana Pombo lab
+      - To be confirmed - in situ ChIA-PET from Ruan lab
+      - Feature maps from Hi-C datasets
+      - TSA-Seq. (Andy mentioned that they were trying to put out Version 2 protocol)
+      - sciHi-C (from Jay Shendure lab)
+      - micro-C (data generated, submitted, not discussed)
+      - Cut & Run (data generated, submitted, needs recommendation and approval)
+      - Trac-loop
+      - MARGI (from Sheng Zhong lab, data generated, submitted)
+  - Need to look at the SC minutes to see which protocols are in production, and approved. (DNase-HiC, in situ HiC, DamID, repli-seq, ChIA-PET)
+      - Additional techniques that have data submitted but need approval
+        - Someone from DCIC can help.
+  - Any additional omic standards to be discussed?\\ DCIC topic - what constitute a replicate set?\\ Protocol.io. Protocol hubs?
-**Agenda - **
+\\ Action items -
-  -
+  - for Bing and Erez the PIs for future presentations.
+  - Make final recommendations for a few methods that have been discussed but not yet received final approval.
-**Schedule for future presentations**
+^Date^Experimental methods^Presenting groups|
-      -
-**March 25: PLAC-seq/HiChIP standard presentation by Miao Yu**
-      -
-**May 27th:  GAM standard presentation by Ana Pombo lab**
-      -
-**To be confirmed - in situ ChIA-PET from Ruan lab**
-      -
-**Feature maps from Hi-C datasets**
-      -
-**TSA-Seq.  (Andy mentioned that they were trying to put out Version 2 protocol)**
-      -
-**sciHi-C (from Jay Shendure lab) **
-      -
-**micro-C (data generated, submitted, not discussed)**
-      -
-**Cut & Run (data generated, submitted, needs recommendation and approval)**
-      -
-**Trac-loop **
-      -
-**MARGI (from Sheng Zhong lab, data generated, submitted)**
-  -
-**Need to look at the SC minutes to see which protocols are in production, and approved.  (DNase-HiC, in situ HiC, DamID, repli-seq, ChIA-PET)**
-      -
-**Additional techniques that have data submitted but need approval**
-        -
-**Someone from DCIC can help. **
-  -
-**Any additional omic standards to be discussed?**
-**DCIC topic - what constitute a replicate set?**
-**Protocol.io.  Protocol hubs?**
-\\ **Action items - **
-  -
-**for Bing and Erez the PIs for future presentations. **
-  -
-**Make final recommendations for a few methods that have been discussed but not yet received final approval.**
-\\ |~~TABLE_CELL_WRAP_START~~<WRAP>
-**Date**
-</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Experimental methods**
-</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Presenting groups**
-</WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**3/25/2019**
+/25/2019
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**PLAC-seq/HiChIP**
+PLAC-seq/HiChIP
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Ren**
+Ren
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**4/22/2019**
+/22/2019
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**5/27/2019**
+/27/2019
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**GAM**
+GAM
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Pombo**
+Pombo
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**6/24/2019**
+/24/2019
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**7/22/2019**
+/22/2019
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
@@ Line 119: / Line 68: @@
 |~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
-**Table below was copied from previous document (circa. 2017)**
+Table below was copied from previous document (circa. 2017)
-|~~TABLE_CELL_WRAP_START~~<WRAP>
+^~~TABLE_CELL_WRAP_START~~<WRAP>
-**OMICS technologies**
+OMICS technologies
-</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
+</WRAP>~~TABLE_CELL_WRAP_STOP~~^~~TABLE_CELL_WRAP_START~~<WRAP>
-**Practicing Group(s)**
+Practicing Group(s)
-</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
+</WRAP>~~TABLE_CELL_WRAP_STOP~~^~~TABLE_CELL_WRAP_START~~<WRAP>
-**Presentation date (protocols need to be shared in advance)**
+Presentation date (protocols need to be shared in advance)
-</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
+</WRAP>~~TABLE_CELL_WRAP_STOP~~^~~TABLE_CELL_WRAP_START~~<WRAP>
-**Person in charge of presenting the protocols**
+Person in charge of presenting the protocols
-</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
+</WRAP>~~TABLE_CELL_WRAP_STOP~~^~~TABLE_CELL_WRAP_START~~<WRAP>
-**Production**
+Production
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**PLAC-seq/HiChIP**
+PLAC-seq/HiChIP
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Ren, Lis, Wysocka/Adelman, Cairns, Neugebauer/Steitz, Yue**
+Ren, Lis, Wysocka/Adelman, Cairns, Neugebauer/Steitz, Yue
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Small working group to be formed by the practicing labs**
+Small working group to be formed by the practicing labs
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**Micro-C**
+Micro-C
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Rando**
+Rando
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**DNase-HiC**
+DNase-HiC
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Duan/Shendure, Disteche, Murry**
+Duan/Shendure, Disteche, Murry
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Nov 13, 2017**
+Nov 13, 2017
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Ramani**
+Ramani
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**scHi-C combinatorial indexing**
+scHi-C combinatorial indexing
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Duan/Shendure**
+Duan/Shendure
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Nov 13, 2017**
+Nov 13, 2017
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Ramani**
+Ramani
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**Single cell Hi-C **
+Single cell Hi-C
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Fraser**
+Fraser
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**March 12, 2018**
+March 12, 2018
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**X**
+X
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**Single nucleus HiC**
+Single nucleus HiC
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Ren**
+Ren
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**ATAC-see**
+ATAC-see
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Chang**
+Chang
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**SPRITE**
+SPRITE
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Gutman**
+Gutman
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Jan 22, 2018**
+Jan 22, 2018
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**GRO-seq**
+GRO-seq
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Lis, Adelman**
+Lis, Adelman
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**PRO-seq**
+PRO-seq
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Lis**
+Lis
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**TCC**
+TCC
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Chen**
+Chen
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**X**
+X
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**TSA-seq**
+TSA-seq
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Belmont**
+Belmont
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**CUT&RUN**
+CUT&RUN
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Henikoff**
+Henikoff
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**DamID**
+DamID
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**van Steensel**
+van Steensel
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**X**
+X
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**GAM**
+GAM
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Pombo**
+Pombo
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**NAD-seq**
+NAD-seq
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**Paul Kaufman lab**
+Paul Kaufman lab
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
 |~~TABLE_CELL_WRAP_START~~<WRAP>
-**TRAC-loop**
+TRAC-loop
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-**KJ Zhao**
+KJ Zhao
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|

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