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--- 4dn:phase2:working_groups:cell_lines_and_samples [2021/07/29 15:44]
david_gilber [Standard Operating Protocols for Cell Stocking and Maintenance]
+++ 4dn:phase2:working_groups:cell_lines_and_samples [2025/04/22 16:21] (current)
@@ Line 1: / Line 1: @@
 ====== Cells ======
-**Point people/organizers:** //Dave Gilbert, Yarui Diao//
+**Point people/organizer: **//Yarui Diao//
 <font inherit/inherit;;#c0392b;;inherit>**4DN Google Drive folder:**</font> [[https://drive.google.com/drive/folders/12hlDOCN-ulRuri0N4SvjpoWPNJkTdMuW?usp=sharing|https://drive.google.com/drive/folders/12hlDOCN-ulRuri0N4SvjpoWPNJkTdMuW?usp=sharing]]
@@ Line 25: / Line 25: @@
 ===== Objectives =====
-) To continue to manage, answer queries, update protocols, negotiate standard lots of reagents for the 4DN Tier1 and Tier2 cell line in order to define gold standard datasets for data integration. 2) To identify 4DN groups working with common cell systems, and encourage them to work with the Cells WG to establish common protocols that will permit generation of 4DN gold standard datasets for integrative analyses. 3) To establish standard protocols for stocking and maintaining cell samples for the 4DN collaborative projects and establish the metadata requirements for datasets to be designated gold standard datasets for integrative analyses. 5) To establish protocols to engineer and differentiate 4DN approved cell lines and make 4DN members aware of these cell lines to avoid duplication of effort.
+) To answer queries, update protocols, negotiate standard lots of reagents for the 4DN Tier1 and Tier2 cell line in order to define gold standard datasets for data integration. 2) To identify 4DN groups working with common cell systems, and encourage them to work with the Cells WG to establish common protocols that will permit generation of 4DN gold standard datasets for integrative analyses. 3) To establish standard protocols for stocking and maintaining cell samples for the 4DN collaborative projects and establish the metadata requirements for datasets to be designated gold standard datasets for integrative analyses. 5) To establish protocols to engineer and differentiate 4DN approved cell lines and make 4DN members aware of these cell lines to avoid duplication of effort.
 **The mailing list for the working group has been changed. Please use [[cells@4dnucleome.org|]] from now on as the new mailing list address.**
@@ Line 43: / Line 43: @@
 ===== Members =====
-**Co-Chairs:**
+**Chair:**
 Yarui Diao, <yarui.diao@duke.edu>
-Dave Gilbert, <gilbert@sdbri.org>
 ===== Meetings =====
@@ Line 59: / Line 57: @@
 Meeting ID: 944 1941 7579\\ Passcode: 985933
-\\ **KATE RIVERA-NOEL** ([[oh@4dnucleome.org|]])
+\\ **KATE RIVERA-NOEL**  ([[oh@4dnucleome.org|]])
-<font 24px/inherit;;inherit;;inherit>**<font inherit/inherit;;#c0392b;;inherit>BELOW ARE THE INSTRUCTIONS FOR OBTAINING, STOCKING, EXPANDING 4DN TIER1 AND TIER2 CELL LINES INCLUDING REQUIRED SOPS, REAGENT LOT NUMBERS TO GENERATE 4DN GOLD STANDARD DATASETS WITH THESE CELL LINES.</font>**  </font>
+<font 24px/inherit;;inherit;;inherit>**<font inherit/inherit;;#c0392b;;inherit>BELOW ARE THE INSTRUCTIONS FOR STOCKING, EXPANDING 4DN TIER1 AND TIER2 CELL LINES INCLUDING REQUIRED SOPS, REAGENT LOT NUMBERS TO GENERATE 4DN GOLD STANDARD DATASETS WITH THESE CELL LINES.</font>** </font>
-**Tier 1 Lines - CLICK ON LINE FOR THE LATEST 4DN GROWTH SOP NECESSARY FOR GOLD STANDARD DATA PRODUCTION!!! NOTE: For cell lines that use FBS, use the negotiated 4DN lot of FBS.**
+<font 24px/inherit;;inherit;;inherit>**<font inherit/inherit;;#c0392b;;inherit>INSTRUCTIONS FOR OBTAINING CELL LINES, INCLUDING MTAs, ARE FOUND ON THE CELL REPOSITORY WIKI PAGE</font>** </font>
-[[https://drive.google.com/file/d/1dGMJB07NRWZPlxEWLtL8Ddzjg_mhkqvu/view?usp=sharing|H1]] male hESC line
+**Tier 1 Lines - CLICK ON LINE FOR THE LATEST 4DN GROWTH SOP NECESSARY FOR GOLD STANDARD DATA PRODUCTION!!! NOTE: For cell lines that use FBS, use the negotiated 4DN lot of FBS. **Brief 4DN history of Tier1 lines is provided. The top priorities for Tier1 were that they have a (relatively) stable karyotype and can be expandable to large numbers. Secondary issues that excluded lines from Tier1 were onerous MTAs or licences (e.g. Geron hTERT plasmid construct in RPE), derivation from tumors (e.g. HCT116), lack of consent for public sharing of raw DNA sequence reads and mouse cells. 4DN Cells WG is always willing to consider any changes or any additions to Tiered cells line (Tier1 or Tier2).
-[[https://drive.google.com/file/d/19vtG_XgX-mvPbSwbLE0xYmJSlley76DP/view?usp=sharing|GM12878]]
+[[https://drive.google.com/file/d/1SKnx1XE7eYCdC61wECZxZ28_WWhmlpJh/view?usp=sharing|H1]] male hESC line
+**<font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>WA01 (aka H1)</font></font></font>** <font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>was chosen due to its abundance of genomics data. Human ESCs offer differentiation toward many different cell lineages. Cells are immortal, and methods for genome engineering are continuously improving. Both fixed and live imaging have been achieved and the motility of the cells has been addressed with cell density and ROCK inhibition. One disadvantage is that they are more challenging to grow and particularly to maintain in an undifferentiated state but in some cases experienced labs could provide fixed material to less experienced labs.</font></font></font>
+[[https://drive.google.com/file/d/1pubGkERDPGIMLROqF1lqSGgEhdJaCcee/view?usp=sharing|GM12878]]
 (*) [[https://drive.google.com/file/d/1rkK_Tm-fMAJq6GyfTXwxSy4mne0qpwbr/view?usp=sharing|IMR90]] (note particularly restrictive MTA terms)
+**<font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>IMR90 and GM12878.</font></font></font>** <font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>Many investigators feel strongly about these cell lines due to the amount of data available in the worldwide scientific community and the momentum that they have accrued. Disadvantages are that IMR90 is not immortal and may change with passage and will eventually undergo growth senescence, while GM12878 is very difficult to transfect and is a suspension cell line that poses challenges for imaging methods. However, these cell lines will serve a large number of 4DN labs wanting to do big data enabled computational modeling.</font></font></font>
 (*) [[https://drive.google.com/file/d/1x0WQQrMS8DXj4zik_8iEc2kwHs4n_qHz/view?usp=sharing|HFF]]c6
-[[https://drive.google.com/file/d/1Cad3S49jmAuV8wz7x-B0inoltxzT8T4z/view?usp=sharing|WTC-11]] - obtain from CORIELL (NOTE: Please carefully read "[[https://drive.google.com/file/d/1KaSdof1dSPxiTRnrqxHOviAL8FUHcBGx/view?usp=sharing|supplementary information]]" as well!!!!!)
+**<font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>hTERT-HFFc6.</font></font></font>** <font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>Many 4DN imaging applications require flat, adherent cells. hTERT-immortalized HFF cells remain diploid over multiple passages (according to users; no data as yet provided) and garnered the most enthusiasm for this purpose from the feedback we received. Since the most commonly used hTERT plasmid is marketed by Geron and imposes a restrictive licence, hTERT-HFF cell line was immortalized using a modified hTERT construct that is not subject to the Geron licence.</font></font></font>
+[[https://drive.google.com/file/d/1Cad3S49jmAuV8wz7x-B0inoltxzT8T4z/view?usp=sharing|WTC-11]] - obtain from CORIELL
+<font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>**WTC-11**  is an iPSC cell line that is fully consented for public sharing of sequencing data, differentiates well to various lineages, exhibits a stable karyotype, and is amenable to gene editing. Allen Institute for Cell Science has used WTC-11 exclusively in its development of myriad GFP fusion protein expressing lines and establishment of live cell imaging methodologies.</font></font></font>
+**<font inherit/inherit;;#c0392b;;inherit><font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit><font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit>SPECIAL NOTES ON WTC-11:</font></font></font></font></font>**
+<font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit><font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>Both the parental WTC-11 cell line as well as the gene-edited WTC-11 cells lines generated by the Allen Institute for Cell Science (AICS) can be obtained from Coriell. Please use the AICS’s cell culture SOP to culture both the parental and the cell lines in the AICS Cell Collection. The AICS does not recommend thawing the parental WTC-11 cell line using the thawing step outlined in their SOP. Due to slight differences in the banking approach of the parental cell line, they recommend using the thawing step of Coriell’s WTC-11 SOP for optimal post-thaw recovery of the parental WTC-11 cell line. The AICS’s cell culture SOP is periodically updated so always use the link to see the most recent SOP.</font></font></font></font></font>Please carefully read "[[https://drive.google.com/file/d/1RWOTjmSdnJXNYdw3E6vP4iYtdhqFaJMg/view?usp=sharing|supplementary information]]" as well!!!
+<font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit><font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;red;;inherit>IMPORTANTLY: There are several versions of this cell line available. Which version you purchase will depend on what you intend to do, but all use the same cell culture SOP. What follows are general explanations of what is available in the Coriell catalog to assist you in making your choice.</font></font></font></font></font>
+<font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit><font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>WTC-11 cat# GM25256: This is the parental “wild-type” cell line. For most engineering purposes, you will want to start with this cell line. Since this line was deposited to Coriell by the Gladstone Institute instead of the AICS, WTC-11’s culture SOP found at Coriell is quite different from other engineered WTC-11 deposited by AICS. For 4DN “gold standard” datasets, please use AICS’ cell culture SOP for passaging the cells even if you use the parental “wild-type” WTC-11 (GM25256).</font></font></font></font></font>
+<font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit><font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>AICS-0036-006: This cell line expresses cytoplasmic GFP from one allele of the AAVS1 safe harbor and was subjected to the same transfection and expansion process as the other gene-edited cell lines in the AICS Cell Collection. A set of recurrent transcriptome changes were found in these gene-edited cell lines compared to the WTC-11 parental line available on Coriell. These transcriptome changes were traced to passage number. Therefore, some investigators prefer to use AICS-0036-006 as a control.</font></font></font></font></font>
+<font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>AICS FP- fusion protein expressing cell lines (cat# varies): The AICS Cell Collection includes many WTC-11-derived cell lines expressing FP-fusion proteins. The catalog of these lines and their Coriell catalog numbers can be found here (</font></font></font><font 12.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font 11.0pt/";inherit;;inherit>//**[[https://www.allencell.org/cell-catalog.html|AICS]]** //</font></font></font>**//__<font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit> cell catalog</font></font></font>__// ** <font 11.0pt/inherit;;inherit;;inherit><font inherit/";inherit;;inherit><font inherit/inherit;;black;;inherit>).</font></font></font>
 **Tier 2 Lines - CLICK ON LINE FOR THE LATEST 4DN GROWTH SOP!! NOTE: For cell lines that use FBS, use the negotiated 4DN lot of FBS.**
@@ Line 93: / Line 113: @@
 (*) [[https://drive.google.com/file/d/1N8cMf5aPbqFCIzzX0sAnJ9RFYxczg5gp/view?usp=sharing|U2OS]] - obtain from ATCC
-(*) [[https://drive.google.com/file/d/1SirVL5UIpKX87hML8G4NB4zXa2jMLEmA/view?usp=sharing|HCT116]] - obtain from ATCC use modified SOP linked here
+(*) [[https://drive.google.com/file/d/180VRga-Sn0siAqRgEeeL2f_XfieONFeg/view?usp=sharing|HCT116]] - obtain from ATCC use modified SOP linked here
 (*) [[https://drive.google.com/file/d/1jOnggGh32lzrL-0UaR1kzGnRuDkuFmFh/view?usp=sharing|JM8.N4]] - mouse ESCs good for imaging, obtain cell line from KOMP, follow SOP linked here, imagers are primarily using serum/LIF recipe
@@ Line 104: / Line 124: @@
 Please refer to the [[https://wiki.4dnucleome.org/4dn:phase2:4dn_cell_repository|4DN Cell Repository wiki page]]
 ===== Consent for lines isolate prior to January 15, 2015 - DISCLAIMER =====
@@ Line 152: / Line 171: @@
 **<font inherit/inherit;;#e74c3c;;inherit>//__FOR ANY OTHER CELL LINES OR OTHER CONDITIONS__//  (e.g. Dox-induction), PLEASE CONTACT TAKAYO SASAKI AT tsasaki@sdbri.org TO DISCUSS TESTING THE LOT WITH YOUR CONDITIONS.</font>**
-[[https://drive.google.com/file/d/1Vxg-e5ZE4qa7OR5__TMy3NOTeXO0unMC/view?usp=sharing|ORDERING INFORMATION FOR FETAL BOVINE SERUM (FOR all Tier1 and Tier2 lines that use serum)]]
+[[https://drive.google.com/file/d/1muFAGTmoK-ecCDBWa0p2TIGX-iBhO5oB/view?usp=sharing|ORDERING INFORMATION FOR FETAL BOVINE SERUM (FOR all Tier1 and Tier2 lines that use serum)]]
-[[https://drive.google.com/file/d/1YFL-E611tn8RFB9zYvEdPmSUB44OKNkj/view?usp=sharing|4DN PHASE2 FBS EVALUATION DATA]]
+[[https://drive.google.com/file/d/1JapYvpv_nijcqH2NiclvnJSN1T9-WEcX/view?usp=sharing|4DN PHASE2 FBS EVALUATION DATA]]
 **hPSC REAGENT INFORMATION**
-[[https://drive.google.com/file/d/16EA9CCz2Ko_4fP06RzftHPxUCRyRv6AN/view?usp=sharing|Stem Cell Tech Quote, which contains ordering instructions]]
+[[https://drive.google.com/file/d/1Ltw48ZOFn-qDi4RpH3-BPK6qBnIbFYWv/view?usp=drive_link|Stem Cell Tech Quote, which contains ordering instructions]]
 Any new PIs joining 4DN recently who are not on this quote can be added to this quote. Please contact Takayo Sasaki <tsasaki@sdbri.org>
@@ Line 174: / Line 193: @@
 **FOR THE LATEST 4DN GROWTH SOP FOR EACH CELL LINE CLICK ON THE CELL LINE IN THE ABOVE LIST OF TIER1 AND TIER2 CELL LINES. **
-=====   =====
+=====  =====
 ===== Standard Operating Protocols for Differentiation of 4DN Cell Lines =====

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