The Jackson Laboratory

Optogenetics Strains

Selected publications featuring JAX optogenetic models

Here we present a selection of published work led by recipients of the 2026 Nobel Prize in Physiology and Medicine – awarded for optogenetics: Stanford University researcher Dr. Karl Deisseroth, Dr. Peter Hegemann from Humboldt University and Dr. Georg Nagel from University of Würzburg. Each of these publications has leveraged a JAX model for optogenetics to support their discoveries!

  • Mimicking opioid analgesia in cortical pain circuits — Corinna Oswell et al. (2026). Nature. Jan;649(8098):938-947. PMID: 41501467
  • Serotonergic neuron-glioma interactions drive high-grade glioma pathophysiology — Richard Drexler et al. (2025). bioRxiv. Dec 12:2025.12.10.693579. PMID: 41427306
  • Two genetically, anatomically and functionally distinct cell types segregate across anteroposterior axis of paraventricular thalamus — Claire Gao, Yan Leng, Jun Ma, Victoria Rooke, Shakira Rodriguez-Gonzalez, Charu Ramakrishnan, Karl Deisseroth, Mario A Penzo (2020). Nat Neurosci. Feb;23(2):217-228. PMID: 31932767
  • BiPOLES is an optogenetic tool developed for bidirectional dual-color control of neurons — Johannes Vierock et al. (2021). Nat Commun. Jul 26;12(1):4527. PMID: 34312384
  • Cortical Observation by Synchronous Multifocal Optical Sampling Reveals Widespread Population Encoding of Actions — Isaac Kauvar, Timothy Machado, Elle Yuen, John Kochalka, Minseung Choi, William Allen, Gordon Wetzstein, Karl Deisseroth (2020). Jul 22;107(2):351-367.e19. PMID: 32433908
  • A Molecular Calcium Integrator Reveals a Striatal Cell Type Driving Aversion — Christina Kim, Mateo Sanchez, Paul Hoerbelt, Lief Fenno, Robert Malenka, Karl Heisseroth, Alice Ting (2020). Cell. Dec 23;183(7):2003-2019.e16. PMID: 33308478
  • Optimized photo-stimulation of halorhodopsin for long-term neuronal inhibition — Chuanqiang Zhang, Shang Yang, To Flossmann, Shiqiang Gao, Otto Witte, Georg Nagel, Knut Holthoff, Knut Kirmse (2019). BMC Biol. Nov 27;17(1):95. PMID: 31775747
  • Optogenetic interrogation of neural circuits: technology for probing mammalian brain structures — Feng Zhang, Viviana Gradinaru, Antoine R Adamantidis, Remy Durand, Raag D Airan, Luis de Lecea, Karl Deisseroth (2010). Nat Protoc. Mar;5(3):439-56. PMID: 20203662

Optogenetic mouse strains

Explore JAX mouse strains used for optogenetics research, organized by genetic control and experimental application.

Availability notes: ∗ Cryopreserved strain. † Available only to nonprofit organizations. A strain may have both symbols.

Cre-Inducible Lines

Common name / JAX #PromoterEffectorExpressionStrain nomenclature
Ai35D∗†
012735		R26 :: CAGArch / GFPCre-dependent ; opsin/xFPB6;129S-Gt(ROSA)26Sortm35.1(CAG-aop3/GFP)Hze/J
Ai40D†
021188		R26 :: CAGArchT / EGFPCre-dependent ; opsin/xFPB6.Cg-Gt(ROSA)26Sortm40.1(CAG-aop3/EGFP)Hze/J
2xChETA-tdT∗
017455		R26 :: CAGChETA/ChR2*H134R and tdTomCre-dependent ; opsin/xFPB6;129-Gt(ROSA)26Sortm1(CAG-COP4*E123T*H134R,-tdTomato)Gfng/J
Ai32†
024109		R26 :: CAGChR2*H134R / EYFPCre-dependent ; opsin/xFPB6.Cg-Gt(ROSA)26Sortm32(CAG-COP4*H134R/EYFP)Hze/J
Ai27D∗†
012567		R26 :: CAGhChR2*H134R / tdTomatoCre-dependent ; opsin/xFPB6.Cg-Gt(ROSA)26Sortm27.1(CAG-COP4*H134R/tdTomato)Hze/J
R26-CAG-LNL-GtACR1-ts-FRed-Kv2.1∗
033089		R26 :: CAGGtACR1 / FusionRedCre-dependent ; opsin/xFP [soma]B6;129S6-Gt(ROSA)26Sortm3Ksvo/J
Rosa26 CAG-LSL-ReaChR-mCit∗
026294		R26 :: CAGReaChR / mCitrineCre-dependent ; opsin/xFPB6.Cg-Gt(ROSA)26Sortm2.2Ksvo/J
Ai39†
014539		R26 :: CAGeNpHR3.0 / EYFPCre-dependent ; opsin/xFPB6;129S-Gt(ROSA)26Sortm39(CAG-hop/EYFP)Hze/J
R26-CAG-lsl-CaMPARI2∗
034240		R26 :: CAGCaMPARI2Cre-dependent ; calcium indicator / photoconvertible xFPB6.Cg-Gt(ROSA)26Sortm1(CAG-Eos*/Calm*)Mrc/J
PC::G5-tdT∗
024477		RNA pol II :: CAGGCaMP5G and tdTomatoCre-dependent ; calcium indicator / xFPB6;129S6-Polr2aTn(pb-CAG-GCaMP5g,-tdTomato)Tvrd/J
Ai95D (C57BL/6J)†
028865		R26 :: CAGGCaMP6fCre-dependent ; calcium indicatorB6J.Cg-Gt(ROSA)26Sortm95.1(CAG-GCaMP6f)Hze/MwarJ
R26-Lck-GCaMP6f flox∗
029626		R26 :: CAGGCaMP6f [membrane]Cre-dependent ; calcium indicator [membrane]C57BL/6N-Gt(ROSA)26Sortm1(CAG-GCaMP6f)Khakh/J
LSL-Salsa6f
031968		R26 :: CAGGCaMP6f / tdTom (Salsa6f)Cre-dependent ;
ratiometric calcium indicator [green/red]		B6(129S4)-Gt(ROSA)26Sortm1.1(CAG-tdTomato/GCaMP6f)Mdcah/J
Ai96 (C57BL/6J)†
028866		R26 :: CAGGCaMP6sCre-dependent ; calcium indicatorB6J.Cg-Gt(ROSA)26Sortm96(CAG-GCaMP6s)Hze/MwarJ
iMb2-Control-Mosaic::
031298		R26 :: CAGMb2-mYFP*A206K ; Mb2-tdTomato ; Mb2-mTFP1 ::
H2B-mCherry ; H2B-EGFP ;
H2B-mCerulean		Cre-dependent ;
mosiac xFP [membrane or chromatin/nuclear]		STOCK Gt(ROSA)26Sortm1(CAG-EYFP*,-mEYFP*,-tdTomato*,-mTFP1*)Ben/Gt(ROSA)26Sortm2(CAG-EYFP*,-mCherry*,-EGFP*,-mCerulean*)Ben/J
iMb2-Control-Mosaic∗
031301		R26 :: CAGMb2-mYFP*A206K ; Mb2-tdTomato ; Mb2-mTFP1Cre-dependent ; mosiac xFP [membrane]STOCK Gt(ROSA)26Sortm1(CAG-EYFP*,-mEYFP*,-tdTomato*,-mTFP1*)Ben/J
iChr2-Control-Mosaic∗
031302		R26 :: CAGH2B-mCherry ; H2B-EGFP ;
H2B-mCerulean		Cre-dependent ;
mosiac xFP [chromatin/nuclear]		STOCK Gt(ROSA)26Sortm2(CAG-EYFP*,-mCherry*,-EGFP*,-mCerulean*)Ben/J
Rosa26LSL-INDIA∗
032068		R26 :: CAGINDIA (mNeonGreen-aCasp3-mRuby2)Cre-dependent ; fluorescent apoptosis reporterB6.Cg-Gt(ROSA)26Sortm1(CAG-mNeonGreen/mRuby2)Mnz/J
TB (tTA2-BFP)∗
031776		H11 :: CAGH2B-mTagBFP + tTA2Cre-dependent xFP [nuclear] and tTAB6;129-Igs2tm5(CAG-tTA2,-TagBFP)Luo/J
Rosa26-CAGs-LSL-RIK
029633		R26 :: CAGmKate2 + rtTA3Cre-dependent xFP and rtTAB6.Cg-Gt(ROSA)26Sortm2(CAG-rtTA3,-mKate2)Slowe/J
CAMPER∗
032205		R26 :: CAGTEpacVV (cAMP FRET sensor)Cre-dependent ; fluorescent cAMP reporterC57BL/6-Gt(ROSA)26Sortm1(CAG-ECFP*/Rapgef3/Venus*)Kama/J
CAG-Sun1/sfGFP
030952		R26 :: CAGSunTag / superfolder GFPCre-dependent ; inner nuclear membrane tagB6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ
SPH∗
031645		CAGSunTag-p65-HSF1Cre-dependent ; dCas9 and xFPB6;D2-Gm33925Tn(pb-CAG-cas9*,-EGFP)1Yangh/J
Ai34D∗
012570		R26 :: CAGSynaptophysin / tdTomatoCre-dependent ; xFP [synapse]B6;129S-Gt(ROSA)26Sortm34.1(CAG-Syp/tdTomato)Hze/J
Ai14
007914		R26 :: CAGtdTomatoCre-dependent ; xFPB6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J

Cre:Tet-Inducible Lines from Allen Institute

Common name / JAX #PromoterEffectorExpressionStrain nomenclature
Ai93D;CaMK2a-tTA∗†
024108		TIGRE :: TRE ; CaMK2aGCaMP6f + tTAforebrain calcium indicator before doxSTOCK Igs7tm93.1(tetO-GCaMP6f)Hze Tg(Camk2a-tTA)1Mmay/J
Ai162D†
031562		TIGRE :: TRE2 + CAGGCaMP6s + tTA2sCre- and Tet-dependent ; calcium indicatorB6.Cg-Igs7tm162.1(tetO-GCaMP6s,CAG-tTA2)Hze/J
Ai148D†
030328		TIGRE :: TRE2 + CAGGCaMP6f + tTA2Cre- and Tet-dependent ; calcium indicatorB6.Cg-Igs7tm148.1(tetO-GCaMP6f,CAG-tTA2)Hze/J
Ai94D;CaMK2a-tTA∗†
024115		TIGRE :: TRE ; CaMK2aGCaMP6s + tTAforebrain calcium indicator before doxB6.Cg-Igs7tm94.1(tetO-GCaMP6s)Hze Tg(Camk2a-tTA)1Mmay/J
Ai143D∗†
030217		TIGRE :: TRERCaMP1.07Cre- and Tet-dependent ; calcium indicator [red]B6.Cg-Igs7tm143.1(tetO-RCaMP1.07)Hze/J
Ai139D∗†
030219		TIGRE :: TRE2 + CAGEGFP + tdT + tTA2Cre- and Tet-dependent ; differential xFPB6.Cg-Igs7tm139.1(tetO-EGFP,CAG-tdTomato,-tTA2)Hze/J
Ai140D∗†
030220		TIGRE :: TRE2 + CAGEGFP + tTA2Cre- and Tet-dependent ; xFPB6.Cg-Igs7tm140.1(tetO-EGFP,CAG-tTA2)Hze/J

Cre:FLP Dual Inducible Lines

Common name / JAX #PromoterEffectorExpressionStrain nomenclature
Ai80D∗†
025109		R26 :: CAGCatCh (ChR2*L132C) / EYFPCre- and FLP-dependent ; opsin/xFPB6.Cg-Gt(ROSA)26Sortm80.1(CAG-COP4*L132C/EYFP)Hze/J
Rosa26 CAG-FSF-LSL-ReaChR-mCit∗
024846		R26 :: CAGReaChR / mCitrineCre- and FLP-dependent ; opsin/xFPB6;129S-Gt(ROSA)26Sortm2.1Ksvo/J
RC::FPSit∗
030206		R26 :: CAGSynaptophysin / EGFP + tdTomatoCre- and FLP-dependent ; xFP [synapse]B6;129S6-Gt(ROSA)26Sortm10(CAG-Syp/EGFP*,-tdTomato)Dym/J
Ai65D†
021875		R26 :: CAGtdTomatoCre- and FLP-dependent ; xFPB6;129S-Gt(ROSA)26Sortm65.1(CAG-tdTomato)Hze/J
RC::FLTG
026932		R26 :: CAGtdTomato ; EGFPFLP-dependent tdT ; then Cre-dependent EGFPB6.Cg-Gt(ROSA)26Sortm1.3(CAG-tdTomato,-EGFP)Pjen/J

Voltage Indicators : OptoPatch, CaViAr and ASAP2s

Common name / JAX #PromoterEffectorExpressionStrain nomenclature
Floxopatch, Optopatch2∗†
028678		R26 :: CAGCheRiff-eGFP :: QuasAr2-mOrange2Cre-dependent ; all-optical electrophysiologyB6;129S6-Gt(ROSA)26Sortm1Acoh/J
Optopatch3 Ai155∗†
029679		TIGRE :: TRECheRiff-eGFP :: QuasAr3-mCitrineCre- & Tet-dependent ; all-optical electrophysiologyB6;129S6-Igs7tm3(tetO-Optopatch3,CAG-tTA)Acoh/J
Ai169D
031569		TIGRE :: TRE2 + CAGASAP2s + tTA2sCre- and Tet-dependent ; voltage indicatorB6.Cg-Igs7tm169.1(tetO-GFP*/TPTE2*,CAG-tTA2)Hze/J

Chemogenetic Lines

Common name / JAX #PromoterEffectorExpressionStrain nomenclature
R26-LSL-Gq-DREADD
026220		R26 :: CAGactiv. Gq-DREADD (hM3Dq) :: mCitrineCre-inducible mCitrine ; then CNO-inducible canonical Gq pathway (burst firing)B6N;129-Tg(CAG-CHRM3*,-mCitrine)1Ute/J
RC::L-hM3Dq∗
026943		R26 :: CAGactiv. Gq-DREADD (hM3Dq) / mCherryCre-inducible mCherry ; then CNO-inducible canonical Gq pathway (burst firing)B6.Cg-Gt(ROSA)26Sortm3.3(CAG-EGFP,-CHRM3*/mCherry/Htr2a)Pjen/J
R26-LSL-Gi-DREADD
026219		R26 :: CAGinhib. Gi-DREADD (hM4Di) :: mCitrineCre-inducible mCitrine ; then CNO-inducible canonical Gi pathway (neuron silencing)B6N.129-Gt(ROSA)26Sortm1(CAG-CHRM4*,-mCitrine)Ute/J
RC::FPDi∗
029040		R26 :: CAGinhib. Gi-DREADD (hM4Di) :: mCherryFLP-inducible mCherry, then Cre- & CNO-inducible canonical Gi pathway (neuron silencing)B6;129S6-Gt(ROSA)26Sortm9(CAG-mCherry,-CHRM4*)Dym/J

Specific Promoter Lines

Common name / JAX #PromoterEffectorExpressionStrain nomenclature
Thy1-ChR2-EYFP line 18
007612		thymus cell antigen 1ChR2 / EYFPwidespread brain ; opsin/xFPB6.Cg-Tg(Thy1-COP4/EYFP)18Gfng/J
Thy1-ChR2-EYFP line 9∗
007615		thymus cell antigen 1ChR2 / EYFPwidespread brain ; opsin/xFPB6.Cg-Tg(Thy1-COP4/EYFP)9Gfng/J
ChAT-ChR2(H134R)-EYFP line 6∗
014546		choline acetyltransferasemhChR2 / EYFPcholinergic neurons ; opsin/xFPB6.Cg-Tg(Chat-COP4*H134R/EYFP,Slc18a3)6Gfng/J
VGAT-ChR2(H134R)-EYFP
014548		vesicular GABA transportermhChR2 / EYFPGABAergic interneurons ; opsin/xFPB6.Cg-Tg(Slc32a1-COP4*H134R/EYFP)8Gfng/J
M72-IRES-ChR2-YFP∗
021206		olfactory receptor 160ChR2*H134R / EYFPM72+ olfactory sensory neurons ; opsin/xFPSTOCK Olfr160tm1.1(COP4*/EYFP)Tboz/J
TRE-GCaMP6s line G6s2
024742		TREGCaMP6sTet-inducible ; calcium indicatorB6;DBA-Tg(tetO-GCaMP6s)2Niell/J
Snap25-2A-GCaMP6s-D∗†
025111		synaptosomal-assoc. prot.25GCaMP6swidespread brain ; calcium indicatorB6.Cg-Snap25tm3.1Hze/J
Cdh5-GCaMP8∗
033342		cadherin 5GCaMP8blood/brain barrier (endothelial cells)B6;SJL-Tg(Cdh5-GCaMP8)B20-6Mik/J
Thy1-jRGECO1a-WPRE, line GP8.20∗
030525		thymus cell antigen 1jRGECO1abrain (denser cortex) ; calcium indicator [red]STOCK Tg(Thy1-jRGECO1a)GP8.20Dkim/J
Thy1-jRGECO1a-WPRE, line GP8.31∗
030526		thymus cell antigen 1jRGECO1abrain (sparser cortex) ; calcium indicator [red]STOCK Tg(Thy1-jRGECO1a)GP8.31Dkim/J
Thy1-jRGECO1a-WPRE, line GP8.58∗
030527		thymus cell antigen 1jRGECO1abrain ; calcium indicator [red]C57BL/6J-Tg(Thy1-jRGECO1a)GP8.58Dkim/J
Thy1-jRGECO1a-WPRE, line GP8.62∗
030528		thymus cell antigen 1jRGECO1abrain ; calcium indicator [red]STOCK Tg(Thy1-jRGECO1a)GP8.62Dkim/J
PrismPlus∗
031478		Cx3cr1 ::
Snap25 :: Mobp :: Aldh1L1		EGFP ::
YFP :: Cerulean :: DsRedMax		microglia ::
neurons :: oligodendrocytes :: astrocytes		STOCK Cx3cr1tm1Litt Tg(Prism)1989Htz/J
mito::mKate2
032188		CAGmKate2widespread fluorescence in mitochondriaSTOCK Tg(CAG-mKate2)1Poche/J
UBC PA-GFP∗
022486		human ubiquitin CPA-GFPwidespread photo-activatable xFPB6.Cg-Ptprca Tg(UBC-PA-GFP)1Mnz/J

Thy1-GCaMP6 Lines from GENIE Project (Janelia/HHMI)

Common name / JAX #PromoterEffectorExpressionStrain nomenclature
GP4.3
024275		thymus cell antigen 1GCaMP6shigh (hippocampus); mod (M1 S1 V1)C57BL/6J-Tg(Thy1-GCaMP6s)GP4.3Dkim/J
GP4.12∗
025776		thymus cell antigen 1GCaMP6shigh in M1, amygdala, S1, hippocampusC57BL/6J-Tg(Thy1-GCaMP6s)GP4.12Dkim/J
GP5.5∗
024276		thymus cell antigen 1GCaMP6fhigh (hippocampus); mod (M1 S1 V1 amyg ob)C57BL/6J-Tg(Thy1-GCaMP6f)GP5.5Dkim/J
GP5.11∗
024339		thymus cell antigen 1GCaMP6fmoderate in hippocampus, M1, S1, V1, olf. bulbC57BL/6J-Tg(Thy1-GCaMP6f)GP5.11Dkim/J
GP5.17
025393		thymus cell antigen 1GCaMP6fhigh in hippocampus, M1, S1, V1, amygdala, olf. bulbC57BL/6J-Tg(Thy1-GCaMP6f)GP5.17Dkim/J
 
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