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4dn:phase2:working_groups:cell_lines_and_samples
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4dn:phase2:working_groups:cell_lines_and_samples [2022/01/06 09:54] oh |
4dn:phase2:working_groups:cell_lines_and_samples [2025/04/22 16:21] (current) |
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| ====== Cells ====== | ====== 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]] | <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]] | ||
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| ===== Members ===== | ===== Members ===== | ||
| - | **Co-Chairs:** | + | **Chair:** |
| Yarui Diao, <yarui.diao@duke.edu> | Yarui Diao, <yarui.diao@duke.edu> | ||
| - | |||
| - | Dave Gilbert, <gilbert@sdbri.org> | ||
| ===== Meetings ===== | ===== Meetings ===== | ||
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| **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). | **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/1dGMJB07NRWZPlxEWLtL8Ddzjg_mhkqvu/view?usp=sharing|H1]] male hESC line | + | [[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> | **<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/19vtG_XgX-mvPbSwbLE0xYmJSlley76DP/view?usp=sharing|GM12878]] | + | [[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) | (*) [[https://drive.google.com/file/d/1rkK_Tm-fMAJq6GyfTXwxSy4mne0qpwbr/view?usp=sharing|IMR90]] (note particularly restrictive MTA terms) | ||
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| **<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 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/1KaSdof1dSPxiTRnrqxHOviAL8FUHcBGx/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;;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;;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> | ||
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| (*) [[https://drive.google.com/file/d/1N8cMf5aPbqFCIzzX0sAnJ9RFYxczg5gp/view?usp=sharing|U2OS]] - obtain from ATCC | (*) [[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 | (*) [[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 | ||
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| **<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>** | **<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/1uewe5pYUHSFVSqiql68SPN_Tf27cG-nV/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** | **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> | 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> | ||
4dn/phase2/working_groups/cell_lines_and_samples.1641491675.txt.gz · Last modified: 2025/04/22 16:21 (external edit)