Resource table {#s0005}
==============

Name of stem cell lineKCL040InstitutionKing\'s College London, London UKDerivation teamNeli Kadeva, Victoria Wood, Glenda Cornwell, Stefano Codognotto, Emma StephensonContact person and emailDusko Ilic, email: <dusko.ilic@kcl.ac.uk>Date archived/stock dateFeb 03, 2012Type of resourceBiological reagent: cell lineSub-typeHuman pluripotent stem cell lineOriginHuman embryoKey marker expressionPluripotent stem cell markers: NANOG, OCT4, TRA-1-60, TRA-1-81, alkaline phosphatase (AP) activityAuthenticationIdentity and purity of line confirmedLink to related literature (direct URL links and full references)1)Jacquet, L., Stephenson, E., Collins, R., Patel, H., Trussler, J., Al-Bedaery, R., Renwick, P., Ogilvie, C., Vaughan, R., Ilic, D., 2013. Strategy for the creation of clinical grade hESC line banks that HLA-match a target population. EMBO Mol. Med. 5 (1), 10--17.doi: 10.1002/emmm.201201973 <http://www.ncbi.nlm.nih.gov/pubmed/23161805>\
2)Canham, A., Van Deusen, A., Brison, D.R., De Sousa, P., Downie, J., Devito, L., Hewitt, Z.A., Ilic, D., Kimber, S.J., Moore, H.D., Murray, H., Kunath, T., 2015. The molecular karyotype of 25 clinical-grade human embryonic stem cells lines. Sci. Rep*.* 5, 17258.doi: 10.1038/srep17258 <http://www.ncbi.nlm.nih.gov/pubmed/26607962>\
3)Ilic, D., Stephenson, E., Wood, V., Jacquet, L., Stevenson, D., Petrova, A., Kadeva, N., Codognotto, S., Patel, H., Semple, M., Cornwell, G., Ogilvie, C., Braude, P., 2012. Derivation and feeder-free propagation of human embryonic stem cells under xeno-free conditions. Cytotherapy. 14 (1), 122--128.doi: 10.3109/14653249.2011.623692\
<http://www.ncbi.nlm.nih.gov/pubmed/22029654>\
4)Stephenson, E., Jacquet, L., Miere, C., Wood, V., Kadeva, N., Cornwell, G., Codognotto, S., Dajani, Y., Braude, P., Ilic, D., 2012. Derivation and propagation of human embryonic stem cell lines from frozen embryos in an animal product-free environment. Nat. Protoc. 7 (7), 1366--1381.doi: 10.1038/nprot.2012.080\
<http://www.ncbi.nlm.nih.gov/pubmed/22722371>Information in public databasesKCL040 is a National Institutes of Health (NIH) registered hESC line\
NIH Registration Number: NIHhESC-14-0272\
<http://grants.nih.gov/stem_cells/registry/current.htm?id=678>EthicsThe hESC line KCL040 is derived under license from the UK Human Fertilisation and Embryology Authority (research licence numbers: R0075 and R0133) and also has local ethical approval (UK National Health Service Research Ethics Committee Reference: 06/Q0702/90).\
Informed consent was obtained from all subjects and the experiments conformed to the principles set out in the WMA Declaration of Helsinki and the NIH Belmont Report. No financial inducements are offered for donation.

Resource details {#s0010}
================

Consent signedSep 03, 2010Embryo thawedJan 17, 2012UK Stem Cell Bank Deposit ApprovalReference: SCSC12-37SexFemale 46, XXGradeClinicalDisease statusHealthy/UnaffectedKaryotype (aCGH)Reduced copy number at 5q13.2 (69,705,561--70,388,844).SNP ArrayCopy-neutral loss of heterozygosity (CN-LOH) at 2q11.1--11.2 (94,871,756--98,412,364), gain at 12p11.21 (31,116,366--31,248,444), loss at 16p11.2 (32,491,547--33,993,220) ([@bb0005])DNA fingerprintAllele sizes (in bp) of 16 microsatellite markers specific for chromosomes 13, 18 and 21 ([@bb0030])HLA typingHLA-A 03, 24; B 07, 15; Bw 4, 6; C 03, 07; DRB1 04, 15; DRB4 01; DRB5 01; DQB1 03, 06 ([@bb0030], [@bb0005])Viability testingPassMycoplasmaNegativeSterilityPassPluripotent markers (immunostaining)\
([Fig. 1](#f0005){ref-type="fig"})NANOG, OCT4, TRA-1-60, TRA-1-81, AP activityThree germ layers differentiation in vitro (immunostaining)\
([Fig. 2](#f0010){ref-type="fig"})Endoderm: AFP\
Ectoderm: TUBB3 (tubulin, beta 3 class III)\
Mesoderm: ACTA2 (actin, alpha 2, smooth muscle)Sibling lines availableNo

We generated KCL040 clinical grade hESC line following protocols, established previously ([@bb0025], [@bb0060]), and now adapted to cGMP conditions. The expression of the pluripotency markers was tested after freeze/thaw cycle ([Fig. 1](#f0005){ref-type="fig"}). Differentiation potential into three germ layers was verified in vitro ([Fig. 2](#f0010){ref-type="fig"}).

Molecular karyotyping using array comparative genomic hybridization aCGH identified reduced copy number at 5q13.2 (69,705,561--70,388,844). The imbalance was not called by software. Whole-genome single nucleotide polymorphism (SNP) array analysis detected CN-LOH at 2q11.1--11.2 (94,871,756--98,412,364), gain at 12p11.21 (31,116,366--31,248,444), loss at 16p11.2 (32,491,547--33,993,220) ([@bb0005]).

This CN-LOH at 2q11.1--11.2 contains multiple genes: *TEKT4*, *MAL*, *MRPS5*, *ZNF514*, *ZNF2*, *PROM2*, *KCNIP3*, *FAHD2A*, *TRIM43*, *ANKRD36C*, *GPAT2*, *ADRA2B*, *ASTL*, *DUSP2*, *STARD7*, *TMEM127*, *CIAO1*, *SNRNP200*, *ITPRIPL1*, *NCAPH*, *NEURL3*, *ARID5A*, *KANSL3*, *FER1L5*, *LMAN2L*, *CNNM4*, *CNNM3*, *ANKRD23*, *ANKRD39*, *SEMA4C*, *FAM178B*, *FAHD2B*, *ANKRD36*, *ANKRD36B*, *COX5B*, *ACTR1B*, *ZAP70*, *TMEM131*, *VWA3B*, and *CNGA3*. Genetic size of this interstitial CN-LOH is relatively small and the double recombination event required to this to happen would be difficult to explain ([@bb0035], [@bb0045]). Therefore, it is unlikely that is acquired ([@bb0005]).

The gain on chromosome 12p11.21 was also found in KCL033. The region contains no genes and it has been also reported in at least 14 submissions at Database of Genomic Variants (DGV; <http://dgv.tcag.ca>), which has collected structural variations in more than 14,000 healthy individuals from worldwide population ([@bb0040]). Estimated frequency in the human population is 4.70% ([@bb0005]).

The loss at 16p11.2 contains three related genes *TP53TG3*, *TP53TG3C*, and *TP53TG3B* and it was reported previously in healthy population ([@bb0055], [@bb0010]). Estimated frequency in the human population is 5.14% ([@bb0005]).

The KCL040 line was negative for Human Immunodeficiency Virus 1 (HIV1), Hepatitis B (HepB, HCB), C Virus (HepC, HCV), Cytomegalovirus (CMV) and Epstein--Barr Virus (EBV) by PCR. Mycoplasma was also not detected.

We also generated research grade of KCL040 line that is adapted to feeder-free conditions.

Materials and methods {#s0015}
=====================

Consenting process {#s0020}
------------------

We distribute Patient Information Sheet (PIS) and consent form to the in vitro fertilization (IVF) patients if they opted to donate to research embryos that were stored for 5 or 10 years. They mail signed consent back to us and that might be months after the PIS and consent were mailed to them. If in meantime new versions of PIS/consent are implemented, we do not send these to the patients or ask them to re-sign; the whole process is done with the version that was given them initially. The PIS/consent documents (FRO-V.8) were created on Mar. 11, 2010. HFEA Code of Practice that was in effect at the time of document creation: Edition 8 --- R.1 (<http://www.hfea.gov.uk/2999.html>). The donor couple signed the consent on Sep. 03, 2010. HFEA Code of Practice that was in effect at the time of donor signature: Edition 8 --- R.2. HFEA Code of Practice Edition 8 --- R.1 was in effect: Oct. 01 2009--Apr. 06, 2010, whereas 8 --- R.2 was in effect: Apr. 07, 2010--Apr. 06, 2011.

Embryo culture and micromanipulation {#s0025}
------------------------------------

Embryo culture and laser-assisted dissection of inner cell mass (ICM) were carried out as previously described in details ([@bb0025], [@bb0060]). The cellular area containing the ICM was then washed and transferred to plates containing mitotically inactivated human neonatal foreskin fibroblasts (HFF).

Cell culture {#s0030}
------------

ICM plated on mitotically inactivated HFF was cultured as described ([@bb0025], [@bb0060]). TE cells were removed mechanically from outgrowth ([@bb0015], [@bb0020]). hESC colonies were expanded and cryopreserved at the third passage.

Viability test {#s0035}
--------------

Straws with the earliest frozen passage (p.2--3) are thawed and new colonies are counted three days later. These colonies are then expanded up to passage 8, at which point cells were part frozen and part subjected to standard battery of tests (pluripotency markers, in vitro and in vivo differentiation capability, genetics, sterility, mycoplasma).

Pluripotency {#s0040}
------------

Pluripotency in vitro was assessed using two different techniques: enzymatic activity assay \[alkaline phosphatase (AP) assay\] and immunostaining as described ([@bb0025], [@bb0060]).

Differentiation {#s0045}
---------------

Spontaneous differentiation into three germ layers was assessed in vitro and in vivo as described ([@bb0050], [@bb0060]). Targeted differentiation in cardiomyocytes followed the protocols described earlier ([@bb0030], [@bb9560]).

Genotyping {#s0050}
----------

DNA was extracted from hESC cultures using a Chemagen DNA extraction robot according to the manufacturer\'s instructions. Amplification of polymorphic microsatellite markers was carried out as described ([@bb0025]). Allele sizes were recorded to give a unique fingerprint of each cell line.

Array comparative genomic hybridization (aCGH) {#s0055}
----------------------------------------------

aCGH was performed as described in details ([@bb0025]).

Whole-genome single nucleotide polymorphism (SNP) array {#s0060}
-------------------------------------------------------

SNP array was performed as described in details ([@bb0005]).

HLA typing {#s0065}
----------

HLA-A, -B and -DRB1 typing was performed with a PCR sequence-specific oligonucleotide probe (SSOP; Luminex, Austin, TX, USA) hybridization protocol at the certified Clinical Transplantation Laboratory, Guy\'s and St Thomas\' NHS Foundation Trust and Serco Plc. (GSTS) Pathology (Guy\'s Hospital, London, UK) as described ([@bb0030]). HLA typing was also performed independently by other group ([@bb0005]).

Special pathology {#s0070}
-----------------

The Doctors Laboratory London (UK) tested the line for HIV1, HepB, HepC, CMV and EBV by PCR.

Author disclosure statement {#s0075}
===========================

There are no competing financial interests in this study.

This work was supported by the UK Medical Research Council grants G0701172 and G0801061. We thank Dr. Yacoub Khalaf, Director of the Assisted Conception Unit of Guy\'s and St Thomas\' NHS Foundation Trust and his staff for supporting the research program. We are especially indebted to Prof Peter Braude and patients who donated embryos.

![Expression of pluripotency markers. Pluripotency is confirmed by immunostaining (Oct4, Nanog, TRA-1-60, TRA-1-81) and alkaline phosphatase (AP) activity assay. Actin stress fibers, visualized with rhodamine-phalloidin (red), are present in both feeders and hES cell colonies, whereas AP activity (green) is detected only in hES cells. Scale bar, 50 μm.](gr1){#f0005}

![Differentiation of three germ layers in vitro is confirmed by detection of markers: smooth muscle actin (red) for mesoderm, β-III tubulin (red) for ectoderm and α-fetoprotein (red) for endoderm. Nuclei are visualized with Hoechst 33,342 (blue). Scale bar, 50 μm.](gr2){#f0010}
