4D Nucleome Network Wiki

4DN Cell Repository

This page describes the ordering process for the established cell lines of the 4DN Cell Repository. The established cell lines specifically refer to the cell lines that have been approved by the Cell Line WG, 4DN steering committee, NIH, and have been ordered by OH or created by 4DN appointed groups.

Eligibility information for PIs who are new to 4DN Cell Repository

All current Phase II PIs have been approved by the Phase II 4DN Cells WG to receive a single vial of each of our commercial repository stocked Tier1 cell lines, including: H1 (WiCell), GM12878 (Coriell), and IMR90 (ATCC). Additional vials will require separate approval from the Cells WG.

NOTE: All PIs are reminded to stock the cells by 4DN standards and to follow the 4DN approved SOP for all cell lines. When data will be submitted to the DCIC, they will need to verify that the cells have been expanded in these conditions that are posted on the Cells WG Wiki page, and the appropriate metadata will need to be recorded at the time of cell harvest in order for datasets to receive the gold standard flag.

Copy of the consent letter for Phase II PIs

Updated agreement/PO with Coriell (9.22.2021)

Consent for lines isolated prior to January 15, 2015 - DISCLAIMER

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

Material Transfer Agreements (MTAs) - DISCLAIMER

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

How to Order Tier 1 and Tier 2 Cells

IMPORTANT! The H1 (WiCell), GM12878 (Coriell), and IMR90 (ATCC) cell lines have been ordered and paid through the 4DN Organization Hub (UC San Diego). WTC-11 is available for purchase at Coriell, the only source of these cells. Each Principal Investigator is responsible for completing and signing the MTAs and for payment of shipping and handling of the cells.

Before thawing the cells

Read the finalized SOP for your cell line from Cell lines WG wiki page. The finalized SOP will provide supplier name with the exact product numbers for the media and matrigel.

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 4DN DATA PORTAL biosample metadata page PAGE EACH TIME YOU START AN EXPERIMENT FOR ANY UPDATES ON REAGENTS, ETC.!!

1. Human embryonic stem cells H1 , by WiCell.AVAILABLE

WICell Ordering Process [WA01 (H1)] (supplementary slides) August 30, 2016. Note that each approved 4DN PI (see below) can order one vial for free, expect for paying the shipping cost
WiCell International Ordering Process (H1)

Request a second vial:

Request a letter of authorization from the OH (oh@4dnucleome.org) and send it by email to Tennielle Ludwig from WiCell (tludwig@wicell.org). After you have send the letter the order procedure is the same.

2. GM12878 , reserved lot by Coriell:AVAILABLE

Passcodes have been sent to all 4DN investigators that requested the GM12878 cells to authorize their purchase

Coriell Ordering Instructions (GM12878)

Protocol to Order GM12878 Cells from Coriell (slides)

International Orders: The same ordering process should be in place, whether the orders are domestic or international. The international investigators still need to provide their unique passcode in the remarks, and they still need to provide a valid shipping account or prepaid label to cover shipping costs. If you have any specific questions regarding shipping, please do not hesitate to reach out to our Customer Service staff, who would be more than glad to assist the PIs. Their contact information is customerservice@coriell.orgcustomerservice@coriell.org or call 1-856-757-4848.

Current PI List that has requested GM12878 Cells as March09, 2018

Request a second vial:

Request a letter of authorization from the OH (oh@4dnucleome.org) and send it by email to Eunice Horton (ehorton@coriell.org) Matt Mitchell (alternate contact) from Coriell (mmitchell@coriell.org). After you have send the letter the order procedure is the same.

3. IMR90 , reserved lot by ATCC:AVAILABLE

Ordering process for customers (Updated process per ATCC on 3.4.2021):

Step 1:

1. Contact Stefan Brings (sbrings@atcc.org) and he will verify that you are on the list of approved consortium members. If you are, Stefan Brings will provide you with the 4DN MTA Addendum. Once the addendum is signed, their Contracts team will review.

4DN Initial Letter ATCC

2. ATCC Contracts will then provide Stefan Brings the approval to send an Order Form to the end user. This Order Form is to be completeed and returned to Stefan Brings.

3. Once Stefan Brings have both the Order Form and the signed Addendum, he will provide these to his team for processing. He will then provide confirmation and estimated ship dates to the end user.

*This entire process can take about 5-10 business days for review and regulatory release of material for shipping. (International orders are more complicated and will likely require permits for shipping and higher courier charges).

Step 2:

1. Stefan will send theATCC Order Form through email.

2. 4DN Member will complete the order form and send it to sales@atcc.org or Fax (703-365-2750) it for a quote (for shipping cost basically).

3. ATCC international order entry team will process the order.

Request a second vial:

Request a letter of authorization from the OH (oh@4dnucleome.org) and send it by email to Stefan Brings from ATCC (sbrings@atcc.org)

4. HFF-hTert-clone 6 reserved lot from UMass .AVAILABLE

The 4DN HFF-hTert-clone 6 Cells will be provided and distributed by Dr. Job Dekker Laboratory free of Charge.

The recipient PI will pay for the shipping of the cells using FedEx or UPS

To request the cells, please contact Johan Gibcus (johan.gibcus@umassmed.edu) from UMass to set up MTA

Ordering Process

5. F121-9 hybrid CASTx129 Female Mouse ESC :AVAILABLE

Contact Dave Gilbert (gilbert@sdbri.org), or Takayo Sasaki (tsasaki@sdbri.org) for cell if any questions.

Simple Letter Agreement (SLA) for CASTx12-F121-9

NOTE : Shoji Takahashi is in charge of the MTAs for the hybrid CASTx129 cells. For more info, Shoji's email: takahash@wi.mit.edu

6. F123 hybrid CASTx129 Male Mouse ESC :AVAILABLE

Contact Bing Ren (biren@health.ucsd.edu) for vials or with questions.

Simple Letter Agreement (SLA) for CASTx12_F123

NOTE: ShojiTakahashi is in charge of the MTAs for the hybrid CASTx129 cells. For more info, Shoji's email: takahash@wi.mit.edu

7. HAP1 Cells: AVAILABLE

HAP1 cells are provided and distributed by the Dr. van Steensel Laboratory from the Netherlands Cancer Institute.

The PI is responsible of the shipping cost

To order the cells and sign MTA contact Dr. Bas van Steensel by email: b.v.steensel@nki.nl

HAP1 Cells_PI List

8. Human embryonic stem cells H9 (female) , by WiCell.AVAILABLE

Obtain from WiCell, use SOP listed on Cells Wiki

9. hTERT-RPE: AVAILABLE