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--- 4dn:phase1:working_groups:omics_data_standards [2019/03/25 15:09]
xiaoyi_cao [Documents]
+++ 4dn:phase1:working_groups:omics_data_standards [2025/04/22 16:21] (current)
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 ====== Omics Data Standards ======
+**The mailing list for the working group has been changed. Please use [[omics@4dnucleome.org|]] from now on as the new mailing list address.**
 ===== Introduction =====
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-**<font 20px/inherit;;#2980b9;;inherit>WEBEX EMERGENCY CONTACT INFORMATION:</font>**
+**<font 20px/inherit;;#2980b9;;inherit>WEBEX CONTACT INFORMATION:</font>**
-**<font 20px/inherit;;#2980b9;;inherit>KATE RIVERA</font>**
+Catherine Rivera-Noel [[oh@4dnucleome.org|]]
-**<font 20px/inherit;;#2980b9;;inherit>858-822-1626 (OFFICE)</font>**
 ===== Documents =====
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-[[:4dn:working_groups:omics_data_standards:minutes-for-2-22|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-for-2-22|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-05-23-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-05-23-2016|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-06-13-2016|Meeting minutes]]\\ Google docs links for [[https://docs.google.com/document/d/1BBHkwrilTaL6N8dQ-QJE5KXKRrZaox3hD7XdEoVyII8/edit?usp=sharing|experiment protocols]] and [[https://docs.google.com/document/d/1WmLyQ7PFQlBn2z4vDMKkmOAxFEZw9dJou7-AjoKHNVs/edit|data formats]], for suggestions and comments
+[[4dn:phase1:working_groups:omics_data_standards:minutes-06-13-2016|Meeting minutes]]\\ Google docs links for [[https://docs.google.com/document/d/1BBHkwrilTaL6N8dQ-QJE5KXKRrZaox3hD7XdEoVyII8/edit?usp=sharing|experiment protocols]] and [[https://docs.google.com/document/d/1WmLyQ7PFQlBn2z4vDMKkmOAxFEZw9dJou7-AjoKHNVs/edit|data formats]], for suggestions and comments
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-[[:4dn:working_groups:omics_data_standards:minutes-06-27-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-06-27-2016|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-07-25-2016|Meeting minutes ]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-07-25-2016|Meeting minutes ]]
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-[[:4dn:working_groups:omics_data_standards:minutes-08-08-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-08-08-2016|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-08-22-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-08-22-2016|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-09-12-2016|Meeting minutes ]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-09-12-2016|Meeting minutes ]]
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-[[:4dn:working_groups:omics_data_standards:minutes-09-26-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-09-26-2016|Meeting minutes]]
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+[[4dn:phase1:working_groups:omics_data_standards:minutes-10-24-2016|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-11-14-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-11-14-2016|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-11-28-2016|Meeting minutes]]\\ Presentation
+[[4dn:phase1:working_groups:omics_data_standards:minutes-11-28-2016|Meeting minutes]]\\ Presentation
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-[[:4dn:working_groups:omics_data_standards:minutes-12-12-2016|Meeting minutes]]\\ Presentation from Suhas Rao
+[[4dn:phase1:working_groups:omics_data_standards:minutes-12-12-2016|Meeting minutes]]\\ Presentation from Suhas Rao
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-[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozYTM1N2M2MzI4MDJkMWI|Draft ChIP-PET protocol (from Y Ruan)]]\\ [[:4dn:working_groups:omics_data_standards:minutes-01-09-2017|Meeting minutes]]
+[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozYTM1N2M2MzI4MDJkMWI|Draft ChIP-PET protocol (from Y Ruan)]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-01-09-2017|Meeting minutes]]
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-Presentation from Rongxin Fang\\ [[:4dn:working_groups:omics_data_standards:minutes-02-13-2017|Meeting minutes]]
+Presentation from Rongxin Fang\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-02-13-2017|Meeting minutes]]
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-[[https://docs.google.com/spreadsheets/d/1eNajg-wroy9Ruj7xAj6i087nm-eM54ueFrBuP5m7JsU/edit?usp=sharing|Spreadsheet for tentative future topics and date]]\\ [[:4dn:working_groups:omics_data_standards:minutes-02-27-2017|Meeting minutes]]
+[[https://docs.google.com/spreadsheets/d/1eNajg-wroy9Ruj7xAj6i087nm-eM54ueFrBuP5m7JsU/edit?usp=sharing|Spreadsheet for tentative future topics and date]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-02-27-2017|Meeting minutes]]
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-[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3OGQxYjE1YmU1NWUzNWYz|Slides for Repli-seq]]\\ [[:4dn:working_groups:omics_data_standards:minutes-03-13-2017|Meeting minutes]]
+[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3OGQxYjE1YmU1NWUzNWYz|Slides for Repli-seq]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-03-13-2017|Meeting minutes]]
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-[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3MWQ2MjlkMDU4OTAzYjBi|DCIC Metadata Slides]]\\ [[:4dn:working_groups:omics_data_standards:minutes-04-10-2017|Meeting minutes]]
+[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3MWQ2MjlkMDU4OTAzYjBi|DCIC Metadata Slides]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-04-10-2017|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-04-24-2017|Meeting minutes]]\\ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo2MmU5ZmEyNGM2OGY5MDJj|DCIC presentation]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-04-24-2017|Meeting minutes]]\\ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo2MmU5ZmEyNGM2OGY5MDJj|DCIC presentation]]
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-[[:4dn:working_groups:omics_data_standards:minutes-05-08-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-05-08-2017|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-05-22-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-05-22-2017|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-06-12-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-06-12-2017|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-06-26-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-06-26-2017|Meeting minutes]]
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-[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo0N2M0MWNkNTlkYjFjM2Qw|DCIC update slides]]\\ [[:4dn:working_groups:omics_data_standards:minutes-07-10-2017|Meeting minutes]]
+[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo0N2M0MWNkNTlkYjFjM2Qw|DCIC update slides]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-07-10-2017|Meeting minutes]]
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-ChIA-PET updated protocol\\ [[https://docs.google.com/a/4dnucleome.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoxYWNiZWJlNmQ2MzEyOWUw|ChIA-PET slides]]\\ [[:4dn:working_groups:omics_data_standards:minutes-07-24-2017|Meeting minutes]]
+ChIA-PET updated protocol\\ [[https://docs.google.com/a/4dnucleome.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoxYWNiZWJlNmQ2MzEyOWUw|ChIA-PET slides]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-07-24-2017|Meeting minutes]]
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-[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo1OGQ5MDU4M2UwMjNhZGNh|DCIC slides]]\\ [[https://docs.google.com/document/d/1ti2YJ-gHSBCBq4DL5iMdCFDE_bQP1LCgJFfEYTte0iY/edit#heading=h.uvjjc19carml|DCIC document ]]\\ [[:4dn:working_groups:omics_data_standards:minutes-08-14-2017|Meeting minutes]]
+[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo1OGQ5MDU4M2UwMjNhZGNh|DCIC slides]]\\ [[https://docs.google.com/document/d/1ti2YJ-gHSBCBq4DL5iMdCFDE_bQP1LCgJFfEYTte0iY/edit#heading=h.uvjjc19carml|DCIC document ]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-08-14-2017|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-08-28-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-08-28-2017|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-10-09-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-10-09-2017|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-10-23-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-10-23-2017|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-11-13-2017|Meeting minutes]]\\ Slides
+[[4dn:phase1:working_groups:omics_data_standards:minutes-11-13-2017|Meeting minutes]]\\ Slides
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-[[:4dn:working_groups:omics_data_standards:minutes-11-27-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-11-27-2017|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-01-08-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-01-08-2018|Meeting minutes]]
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-[[https://drive.google.com/file/d/17hkhfodJ-XnRME38hWfPGWXHAP69IcyR/view|SPRITE protocol]]\\ [[:4dn:working_groups:omics_data_standards:minutes-01-22-2018|Meeting minutes]]
+[[https://drive.google.com/file/d/17hkhfodJ-XnRME38hWfPGWXHAP69IcyR/view|SPRITE protocol]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-01-22-2018|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-02-12-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-02-12-2018|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-02-26-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-02-26-2018|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-03-12-2018|Meeting minutes]]\\ [[https://docs.google.com/a/4dnucleome.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozZjUyMDBkZTk0NTZjZmI4|Presentation for Single cell Hi-C from Peter Fraser Lab]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-03-12-2018|Meeting minutes]]\\ [[https://docs.google.com/a/4dnucleome.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozZjUyMDBkZTk0NTZjZmI4|Presentation for Single cell Hi-C from Peter Fraser Lab]]
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-[[:4dn:working_groups:omics_data_standards:minutes-04-09-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-04-09-2018|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-05-14-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-05-14-2018|Meeting minutes]]
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-[[:4dn:protocols:damid|Wiki page for DamID]]\\ [[:4dn:working_groups:omics_data_standards:minutes-06-11-2018|Meeting minutes]]
+[[4dn:phase1:protocols:damid|Wiki page for DamID]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-06-11-2018|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-06-25-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-06-25-2018|Meeting minutes]]
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-  * Discuss and vote on the DamID protocol (see link [[:4dn:protocols:damid|here]]). This was presented on June 11th.
+  * Discuss and vote on the DamID protocol (see link [[4dn:phase1:protocols:damid|here]]). This was presented on June 11th.
   * Discussion and vote on the Cut&Run protocol (see link [[https://www.google.com/url?q=https://www.nature.com/articles/nprot.2018.015.epdf?author_access_token=vf_ylGdH8oTFIbGYdyahH9RgN0jAjWel9jnR3ZoTv0NOQV_YOinFX53TT-yN_6ziKCqbazelkV5TLOcj4FgNB72aCjfEhYgiGP0HE3gHZJbRtWNmNoZwyH7Y6HToKMfQ&sa=D&sntz=1&usg=AFQjCNECGEGq02z8erEG0gwEFw9TpUF8cA|here]]). This was presented on June 25th.
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-[[:4dn:working_groups:omics_data_standards:minutes-07-23-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-07-23-2018|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-08-13-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-08-13-2018|Meeting minutes]]
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-[[:4dn:working_groups:omics_data_standards:minutes-09-10-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-09-10-2018|Meeting minutes]]
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@@ Line 678: / Line 679: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-11-19-2018|Meeting minutes]]\\ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozZWVjOGY4YTk0Y2RhN2M1|Presentation by Miao Yu.]]~~CKG_TABLE_NBSP~~"Optimization and Comparison of PLAC-seq and HiChIP protocols"
+[[4dn:phase1:working_groups:omics_data_standards:minutes-11-19-2018|Meeting minutes]]\\ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozZWVjOGY4YTk0Y2RhN2M1|Presentation by Miao Yu.]]~~CKG_TABLE_NBSP~~"Optimization and Comparison of PLAC-seq and HiChIP protocols"
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
@@ Line 691: / Line 692: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-01-28-2019|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-01-28-2019|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
@@ Line 704: / Line 705: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-02-25-2019|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-02-25-2019|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
@@ Line 711: / Line 712: @@
   * Update on PLAC-seq / HiChIP protocol
-      * QC metrics
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-      * Recommended antibodies
+[[4dn:phase1:working_groups:omics_data_standards:minutes-03-25-2019|Meeting minutes]]
-      * Crosslinking conditions
+Presentation by Miao Yu
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|
+|~~TABLE_CELL_WRAP_START~~<WRAP>
+=== 2020 Meetings ===
+</WRAP>~~TABLE_CELL_WRAP_STOP~~  |||
+|3-23-2020  |~~TABLE_CELL_WRAP_START~~<WRAP>
+  * Review protocols recommended for 4DN SC
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-03-25-2019|Meeting minutes]]
+[[https://docs.google.com/document/d/1t3fxUTzABezu5fxhH_iAMq1szaojHD8FdUFRs9UWGcI/edit?pli=1|Meeting minutes]]
-Presentation by Miao Yu
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|
+|4-27-2020  |~~TABLE_CELL_WRAP_START~~<WRAP>
+  * <font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit>Review last month’s minutes and action plan.</font></font>
+  * <font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit>Presentation on comparison of ChIA-PET/HiCHIP/PLAC-seq (Dr. Xiaotao Wang from Dr. Feng Yue’s group)</font></font>
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
+[[https://docs.google.com/document/d/1WzKl4ACWO1lxQrMTmEFdF_8N51DArW4-aIMbjeh7siw/edit?pli=1|Meeting minutes]]
+[[https://wiki.4dnucleome.org/_media/4dn:working_groups:omics_data_standards:4dn-pulldown-based-0427.pptx|Presentation by Dr. Xiaotao Wang]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
+|6-22-2020~~CKG_TABLE_NBSP~~  |~~TABLE_CELL_WRAP_START~~<WRAP>
+  * Meeting minutes~~CKG_TABLE_NBSP~~
-===== Listserv =====
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
+[[https://mail.google.com/mail/u/0?ui=2&ik=ed374f079d&attid=0.1&permmsgid=msg-f:1670220830497479983&th=172dd0ff02429d2f&view=att&disp=safe|Discussion on HiChIP/PLAC-seq protocol]]~~CKG_TABLE_NBSP~~
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|
-The Listserv to use for communication in this Working Group is [[4DN-OMICS@list.nih.gov|]]. Emails sent there will go to everyone on the list. Replying to an email from the list will also send it to everyone in the list. [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/omicswg/Detailed Instructions on how to interact with the listserv - Omics.pdf?attredirects=0&d=1|Detailed Instructions on how to interact with the Listserv System are available - Omics]]
+===== Mailing list =====
+The mailing list to use for communication in this Working Group is <omics@4dnucleome.org>. Emails sent there will go to everyone on the list. Replying to an email from the list will also send it to everyone in the list.
 ===== Calendar =====
 {{url>https://calendar.google.com/calendar/embed?src=6it3bntuu76dtpe4odqmoke3l0%40group.calendar.google.com 800,400 noborder|4DN OMICS WG Calendar}}
+----
+{{medialist>4dn:working_groups:omics_data_standards:}}

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