The mailing list for the working group has been changed. Please use cells@4dnucleome.org from now on as the new mailing list address.

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You can find this information in the 4DN wiki > community information > Question 19 on the following page: community_information

One major goal of the 4D Nucleome Network is the development, application and integration of a large array of different technologies to study the structure and dynamics of the human genome. The application of these methods to a small set of common cell lines will greatly facilitate achieving this goal, and will provide at an early stage in the project insights into the synergies as well as challenges in data integration. This working group’s goal is to define common cell lines for study by the Network. These cell lines will be used for cross-consortium integrated analyses, while individual laboratories will also use lab-specific materials selected for their specific project or technology. Individual groups are encouraged to add these common cell lines to the set of cells they already study.

Milestones

1) To identify a small set of cell lines that all participating laboratories in the 4DN network will study.

2) To identify mechanisms to obtain these cells (both fixed and live cells) in large quantities, in a reproducible manner across the network.

3) To establish protocols to coordinate with the DCIC and AWG to collect, integrate, analyze and broadly share all data obtained with these common cell lines.

4) To establish protocols to engineer and differentiate 4DN approved cell lines

4DN Cells Legacy Document

Regular Cells WG meetings will be held on the last Thursday of every month at 11AM PT, 2PM ET.

WEBEX EMERGENCY CONTACT INFORMATION:

KATE RIVERA

858-822-1626 (OFFICE)

Past meetings:

Meeting Minutes: January 18th, 2016 Meeting Minutes

Meeting Minutes: February 9, 2016 Meeting minutes

Meeting Minutes: March 7, 2016

Meeting Minutes: March 31, 2016

Meeting Minutes: April 28, 2016

Meeting Minutes: May 25, 2016

Meeting Minutes: June 30, 2016

Meeting Minutes: July 28, 2016

Meeting Minutes: August 25, 2016

Meeting Minutes: September 29, 2016

Meeting Minutes: October 27, 2016

Meeting Minutes: December 15, 2016

Meeting Minutes: January 26, 2017

Meeting Minutes: February 23, 2017

Meeting Minutes: March 30, 2017

Meeting Minutes: April 27, 2017

Meeting Minutes: May 25, 2017

Meeting Minutes: June 29, 2017

Meeting Minutes: July 27, 2017

Meeting Minutes: August 31, 2017

Meeting Minutes: October 26, 2017

Meeting Minutes: January 25, 2017

Meeting Minutes: March 29, 2018

Meeting Minutes: April 26, 2018

Meeting Minutes: June 28, 2018

Meeting Minutes: September 27, 2018

Meeting Minutes: October 25, 2018

Meeting Minutes: January 24, 2019

Meeting Minutes: February 28, 2019

Meeting MInutes: March 28, 2019

Please refer to the 4DN Cell Repository wiki page

Posting of public data from specimens collected before January 15, 2015 is the responsibility of and must be approved by each PIs institution. Additional questions about Consent should be addressed by individual PIs with their institutions.

Sample Institutional Certification Form for Public sharing of data from specimens collected before January 15, 2015 that lack consent

NIH page of FAQs for Genomic Data Sharing Policy

(EXAMPLE) Florida State University RESEARCH COMPLIANCE page

MTAs are the responsibility of each PI and their institution and are to be negotiated separately between each institution and the distributor. Additional questions about MTAs should be addressed by individual PIs with their institutions. The document below is a list of salient points from the MTAs between the OH (UCSD) and the three major providers, provided to 4DN PIs for your convenience as a courtesy and not to be considered a binding document.

Readers Digest List of MTA Conditions Condensed by the OH

ARE YOU ENGINEERING ANY OF THE 4DN CELL LINES? - please see this discussion group of who is engineering what so as not to duplicate effort or work together!

DATASETS GENERATED USING THE APPROVED SOP PRECISELY AND PROVIDING THE REQUISITE METADATA WILL BE MARKED “GOLD STANDARD” - IF YOU DO NOT FOLLOW THESE PROTOCOLS STRICTLY THEN YOUR DATASETS WILL NOT BE DESIGNATED “GOLD STANDARD”. MAKE SURE TO CHECK THE CELLS WIKI PAGE EACH TIME YOU START AN EXPERIMENT FOR ANY UPDATES ON REAGENTS, ETC.!!

Upon submission of data to the DCC, PIs will be asked to authenticate the cellular material from which data were derived, and whether the handling of the cells deviated from the SOPs provided below, which are intended to minimize variability between labs. Authentication criteria for each cell line may differ. THE SOP FOR EACH LINE CAN BE FOUND BY CLICKING ON THE CELL LINE BELOW.

PYRAMID METHOD TO STOCK MAMMALIAN CELLS (upon receipt of your vial, this is the first thing you must do)

ORDERING INFORMATION FOR FETAL BOVINE SERUM (FOR all Tier1 and Tier2 lines that use serum)

FBS TEST RESULTS FOR IMR90

FBS TEST RESULTS FOR HFFc6

FBS TEST RESULTS FOR GM12878

FBS TEST RESULTS FOR JM8N4

KARYOTYPE INFORMATION FOR NON-COMMERCIALLY STOCKED LINES (HFFc6, F121-9 and F123)

Document on how to read a karyotype report

HFFc6

F121-9

F123

Tier 1 Lines - CLICK ON LINE FOR THE LATEST 4DN GROWTH SOP!!

H1 male hESC line

GM12878

(*) IMR90 (note particularly restrictive MTA terms)

(*) HFFc6

WTC-11 - obtain from CORIELL GM25256 (NOTE: DO NOT USE THE CORIELL GROWTH SOP!!!!!)

Tier 2 Lines - CLICK ON LINE FOR THE LATEST 4DN GROWTH SOP!!

F121-9 female CASTx129 hybrid mouse ESCs - obtain from Dave Gilbert.

F123 male CASTx129 hybrid mouse ESCs - obtain SOP and cell line from Bing Ren

K562 - obtain from ATCC

H9 female hESC line - obtain from Wicell and use same SOP as H1

(*) hTERT-RPE - obtain from ATCC (note particularly restrictive MTA terms)

HEK293 - obtain from ATCC

HAP1 - obtain from van Steensel lab (note particularly restrictive MTA terms)

(*) U2OS - obtain from ATCC

(*) HCT116 - obtain from ATCC use modified SOP linked here

(*) JM8.N4 - mouse ESCs good for imaging, obtain cell line from KOMP, follow SOP linked here, imagers are primarily using serum/LIF recipe

G4 - mouse ESCs that have been extensively engineered by the Ritland/Groudine group. Obtain from Carol Ware: cware@u.washington.edu

(*) These lines are recommended for use in imaging by the Imaging Data Standards Working Group

These are suggested protocols based on first hand experience from 4DN members

High Efficiency Transfection of hESC line H9 (Note: H1 requires a different protocol)

High Efficiency Transfection and CRISPR editing of F121-9

These protocols have been vetted by at least two 4DN laboratories and lots and prices for reagents negotiated. Following these SOPs is necessary for your data to be branded “gold standard”.

Differentiating hESCs to DE

Differentiating mESCs to NPCs

Differentiating mESCs to EpiLCs

H1 male hESC line (H1-derived NPCs)

H9 female hESC line (Other H9 - derived fates)

GM12878

IMR90

K562

HEK293

HAP1

U2OS

HCT116

Co-Chairs:

Job Dekker, job.dekker@umassmed.edu

Dave Gilbert, gilbert@bio.fsu.edu

Add spreadsheet with all the group members

The Listserv to use for communication in this Working Group is cells@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.