| 4OHTAM_100nM_30m |
30 minutes with 100 nM 4-hydroxytamoxifen (Crawford) |
4-OHTAM 100nM 30m |
| 4OHTAM_1uM_12hr |
12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) |
4-OHTAM 1uM 12hr |
| 4OHTAM_1uM_36hr |
(To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) |
4-OHTAM 1uM 36hr |
| 4OHTAM_1uM_4hr |
4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) |
4-OHTAM 1uM 4hr |
| 4OHTAM_20nM_72hr |
72 hours with 20 nM 4-hydroxytamoxifen (Stam) |
4-OHTAM 20nM 72hr |
| Alpha-amanitin_50ug_9hr |
9h with 50 ug/ml alpha-amanitin |
Alpha-amanitin_50ug_9hr |
| androgen |
12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) |
Methyltrienolone |
| Betamethasone_100nM |
1 h with 100 nM Betamethasone (Myers) |
Betamethasone_100nM |
| BPA_100nM |
1 h with 100 nM Bisphenol A (Myers) |
BPA_100nM |
| BPA_100nM_4hr |
4 h with 100 nM Bisphenol A (Myers) |
BPA_100nM_4hr |
| CTCF_shRNA_knockdown |
CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. |
CTCF shRNA knockdown |
| DEX_100nM |
1 h with 100 nM Dexamethasone (Myers) |
DEX_100nM |
| DEX_100pM |
1 h with 100 pM Dexamethasone (Myers) |
DEX_100pM |
| DEX_1nM |
1 h with 1 nM Dexamethasone (Myers) |
DEX_1nM |
| DEX_500pM |
1 h with 500 pM Dexamethasone (Myers) |
DEX_500pM |
| DEX_50nM |
1 h with 50 nM Dexamethasone (Myers) |
DEX_50nM |
| DEX_5nM |
1 h with 5 nM Dexamethasone (Myers) |
DEX_5nM |
| DIFF_4d |
Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) |
DIFF_4d |
| DIFF_7d |
Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) |
DIFF_7d |
| diffProtA_14d |
H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm |
14 day diff protocol A |
| diffProtA_2d |
H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm |
2 day diff protocol A |
| diffProtA_5d |
H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm |
5 day diff protocol A |
| diffProtA_9d |
H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm |
9 day diff protocol A |
| diffProtB_24hr |
Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) |
24 hour diff protocol B |
| diffProtB_6hr |
Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 6 hours. Doxycycline added to a final concentration of 100 ng/ml. (Stam) |
6 hour diff protocol B |
| diffProtB_72hr |
Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 72 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) |
72 hour diff protocol B |
| diffProtC_120hr |
120 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) |
120 hour diff protocol C |
| diffProtC_24hr |
24 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) |
24 hour diff protocol C |
| diffProtC_48hr |
48 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) |
48 hour diff protocol C |
| diffProtD_14hr |
14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) |
Estradiol 14 hour diff protocol |
| diffProtD_24hr |
24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) |
Estradiol 24 hour diff protocol |
| diffProtD_30hr |
30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) |
Estradiol 30 hour diff protocol |
| diffProtD_3hr |
3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) |
Estradiol 3 hour diff protocol |
| diffProtD_7hr |
7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) |
Estradiol 7 hour diff protocol |
| diffProtE_3d |
3 day differentiation of ES-D3 cells with conditioned medium MEDII to form neural precursor cells (Gilbert) |
diffProtE_3d |
| diffProtE_6d |
6 day differentiation of ES-D3 cells with conditioned medium MEDII to form neural precursor cells (Gilbert) |
diffProtE_6d |
| diffProtE_9d |
9 day differentiation of ES-D3 cells with conditioned medium MEDII to form neural precursor cells (Gilbert) |
diffProtE_9d |
| diffProtF_6d |
6 day differentiation of ES-46C cells in adherent monolayer culture (Gilbert) |
diffProtF_6d |
| diffProtF_9d |
9 day differentiation of ES-TT2 cells in adherent monolayer culture (Gilbert) |
diffProtF_9d |
| diffProtG_3d |
3 day differentiation of ES-D3 cells with conditioned medium MEDII to form attached monolayer cells, early primitive ectoderm-like cells (EPL) (Gilbert) |
diffProtG_3d |
| diffProtH_Sox17+ |
Differentiation of ES-GscgfpSox17huCD25 towards endoderm cells after treatment with serum-free medium, SFO3, containing activin (10 ng/ml). After 6 days, cells were collected for Gsc+Sox17+ by fluorescence activated cell sorting (FACS). (Gilbert) |
diffProtH_Sox17+ |
| diffProtH_Sox17- |
Differentiation of ES-GscgfpSox17huCD25 towards mesoderm cells after treatment with serum-free medium, SFO3, containing activin (10 ng/ml). After 6 days, cells were collected for Gsc+Sox17- by fluorescence activated cell sorting (FACS). (Gilbert) |
diffProtH_Sox17- |
| DMSO_0.02pct |
1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) |
DMSO_0.02pct |
| DMSO_0.02pct_24hr |
24 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) |
DMSO_0.02pct_24hr |
| DMSO_0.02pct_7d |
7 d with 0.02% Dimethyl sufloxide (DMSO) (Myers) |
DMSO_0.02pct_7d |
| DMSO_2.0pct |
5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) |
DMSO_2.0pct |
| DMSO_4hr |
4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) |
DMSO_4hr |
| EqS_2.0pct_24hr |
24 h with 2.0% Equine Serum and Insulin (Wold) |
EqS_2.0pct_24hr |
| EqS_2.0pct_5d |
5 d with 2.0% Equine Serum and Insulin (Wold) |
EqS_2.0pct_5d |
| EqS_2.0pct_60hr |
60 h with 2.0% Equine Serum and Insulin (Wold) |
EqS_2.0pct_60hr |
| EqS_2.0pct_7d |
7 d with 2.0% Equine Serum and Insulin (Wold) |
EqS_2.0pct_7d |
| Estradiol_100nM_1hr |
1 h with 100 nM Estradiol, hormone treatment (Stam) |
Estradiol_100nM_1hr |
| Estradiol_10nM |
1 h with 10 nM Estradiol (Myers) |
Estradiol_10nM |
| Estradiol_10nM_24hr |
24 hr with 10 nM Estradiol (Myers) |
Estradiol_10nM_24hr |
| Estradiol_10nM_30m |
30 min with 10nM 7b-Estradiol (Crawford) |
Estradiol_10nM_30m |
| Estradiol_10nM_4hr |
4 h with 10 nM Estradiol (Myers) |
Estradiol_10nM_4hr |
| Estradiol_1nM |
1 h with 1 nM Estradiol (Myers) |
Estradiol_1nM |
| Estradiol_ctrl_0hr |
No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam) |
Estradiol_ctrl_0hr |
| estrogen |
45 min with 100 nM Estradiol (Crawford) |
Estradiol 100 nM |
| EtOH_0.01pct |
36 h with 0.01% Ethanol (Snyder) |
EtOH 0.01% 36h |
| EtOH_0.01pct_12hr |
12 h with 0.01% Ethanol (Snyder) |
EtOH 0.01% 12h |
| EtOH_0.01pct_4hr |
4 h with 0.01% Ethanol (Snyder) |
EtOH 0.01% 4h |
| EtOH_0.02pct |
1 h with 0.02% Ethanol (Myers) |
EtOH 0.02% 1h |
| forskolin |
low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) |
forskolin |
| G1_phase |
Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of the single DNA content peak taken as G1 cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford) |
G1_phase |
| G2-M_phase |
Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of double DNA content taken as G2 and M cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford) |
G2-M_phase |
| Genistein_100nM |
1 h with 100 nM Genistein (Myers) |
Genistein_100nM |
| Genistein_100nM_4hr |
4 h with 100 nM Genistein (Myers) |
Genistein_100nM_4hr |
| Hypoxia_LacAcid |
24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) |
Hypoxia, Lactic acidosis |
| Hypoxia_LacAcid_ctrl |
Untreated cells grown along side Hypoxia LacAcid treated cells (Crawford) |
Untreated control cells |
| IFNa30 |
30 m of Interferon alpha (Snyder) |
IFNa30 |
| IFNa4h |
4 hours of 500 U/ml Interferon alpha (Crawford) |
IFN-a 4 h |
| IFNa6h |
Interferon alpha treatment - 6 hours (Snyder) |
IFNa6h |
| IFNg30 |
Interferon gamma treatment - 30 minutes (Snyder) |
IFNg30 |
| IFNg4h |
Interferon gamma treatment - 4 hours with 5 ng/ml (Crawford) |
IFN-g 4 h |
| IFNg6h |
Interferon gamma treatment - 6 hours (Snyder) |
IFNg6h |
| insulin |
DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder) |
insulin |
| lenti-control |
GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were cultured for 10 days (NO DOXYCYCLINE) (Crawford) |
lenti-control |
| lenti-MyoD |
GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were induced for MYOD expression for 10 days with doxycycline and at concentration of 3ug per ml. Standard media was used (and replaced every 2 days) during induction: DMEM, 1% Pen Strep, and 10% FBS. (Crawford) |
lenti-MyoD |
| MNaseD |
Fragmented using micrococcal nuclease digestion |
Micrococcal nuclease |
| NaBut |
0.5 mM Sodium Butyrate for 72 hours |
Sodium Butyrate |
| OHUrea |
100 uM Hydroxyurea for 72 hours |
Hydroxyurea |
| pravastatin |
For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) |
pravastatin |
| Prednisolone_100nM |
1 h with 100 nM Prednisolone (Myers) |
Prednisolone_100nM |
| Randomized_shRNA_control |
Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. |
Randomized shRNA control |
| SAHA_1uM_72hr |
Cells grown with 1 uM suberoylanilide hydroxamic acid (SAHA) dissolved in DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (SAHA vehicle volume is ~ .05% of the total media volume). SAHA was provided by Cayman Chemical, item # 10009929. |
SAHA 1uM 72hr |
| SAHA_ctrl |
Cells grown with DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (DMSO volume is ~ .05% of the total media volume). This is an untreated control. |
SAHA control |
| serum_free_media |
Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford) |
Serum-free media |
| serum_starved_media |
Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours |
serum-starved media |
| serum_stimulated_media |
Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. |
serum-stimulated media |
| Taxol_500nM_24hr |
500 nM Taxol for 24 hours, then sorted for 4n DNA content (Crawford) |
Taxol 500nM 24hr |
| TGFb |
1 ng/mL transforming growth factor beta for 24 hours (Crawford) |
TGF-beta |
| TNFa |
human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) |
TNF-alpha |
| UT189 |
UT189 E.Coli treatment 1 hour, followed by 24 hour incubation |
UT189 E. coli |
| vehicle |
Charcoal stripped hormone-free FBS for 72 hours (Crawford) |
Vehicle |