DOI: 10.5061/dryad.tk467n8
title: Data from: Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping

description: Decoding the functional connectivity of the nervous system is facilitated
 by transgenic methods that express a genetically encoded reporter or
 effector in specific neurons; however, most transgenic lines show broad
 spatiotemporal and cell-type expression. Increased specificity can be
 achieved using intersectional genetic methods which restrict reporter
 expression to cells that co-express multiple drivers, such as Gal4 and
 Cre. To facilitate intersectional targeting in zebrafish, we have
 generated more than 50 new Cre lines, and co-registered brain expression
 images with the Zebrafish Brain Browser, a cellular resolution atlas of
 264 transgenic lines. Lines labeling neurons of interest can be identified
 using a web-browser to perform a 3D spatial search (zbbrowser.com). This
 resource facilitates the design of intersectional genetic experiments and
 will advance a wide range of precision circuit-mapping studies.
description: rhombomereThis archive contains: y454-eltC (Tg(eltC-REx2-SCP1:BGi-Cre-2a-Cer)y454), N = 3 larval zebrafish; y455-dr16 (Tg(hoxb3a-dr16-SCP1:BGi-Cre-2a-Cer)y455), N = 3; y461-hoxb1a (Tg(hoxb1a-SCP1:BGi-Cre-2a-Cer)y461), N = 5; y466-hoxa2 (Tg(hoxa2CNE-SCP1:BGi-Cre-2a-Cer)y466), N = 4. Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is Tg(elavl3:mCar.zf1)y583 (huC:mCar), and color channel 02 is the Cre expression pattern.y371-y385This archive contains: y371-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y371, N = 4 larval zebrafish; y378-Cre, N = 3; y379-Cre, N = 3; y380-Cre, N = 3; y381-Cre, N = 2; y382-Cre, N = 3; y383-Cre, N = 3; y384-Cre, N = 4; y385-Cre, N = 3. Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #". For most brain images, color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal). For y378-f2, y378-f3, y381-f1 and y381-f2 color channel 01 is Tg(elavl3:mCar.zf1)y583 (huC:mCar) and channel 02 is the Cre expression pattern.y445-y459This archive contains: y445-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y445, N = 3 larval zebrafish; y456-Cre, N = 3; y457-Cre, N = 3; y458-Cre, N = 4; y459-Cre, N = 3. Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is Tg(elavl3:mCar.zf1)y583 (huC:mCar) and channel 02 is the Cre expression pattern.y465-y481This archive contains: y465-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y465, N = 5 larval zebrafish; y478-Cre, N = 3; y479-Cre, N = 3; y480-Cre, N = 3; y481-Cre, N = 4. Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #". For most brain images, color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal). For y465-f5, color channel 01 is Tg(elavl3:mCar.zf1)y583 (huC:mCar) and channel 02 is the Cre expression pattern.y483-y487This archive contains: y483-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y483, N = 3 larval zebrafish; y484-Cre, N = 4; y485-Cre, N = 3; y486-Cre, N = 4; y487-Cre, N = 3. Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).y488-y493This archive contains: y488-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y488, N = 3 larval zebrafish; y489-Cre, N = 4; y490-Cre, N = 3; y492-Cre, N = 3; y493-Cre, N = 3. Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).y494-y521This archive contains: y494-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y494, N = 3 larval zebrafish; y495-Cre, N = 3; y519-Cre, N = 4; y520-Cre, N = 3; y521-Cre, N = 3. Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).y523-y541This archive contains: y523-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y523, N = 5 larval zebrafish; y524-Cre, N = 3; y526-Cre, N = 3; y528-Cre, N = 3; y541-Cre, N = 4. Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).y542-y546This archive contains: y542-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y542, N = 4 larval zebrafish; y543-Cre, N = 4; y544-Cre, N = 4; y545-Cre, N = 10; y546-Cre, N = 5. Image stacks are compressed nifti files (8 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).y547-y552This archive contains: y547-Cre Et(REx2-SCP1:BGi-Cre)y547, N = 4 larval zebrafish; y548-Cre Et(REx2-SCP1:BGi-Cre)y548, N = 4; y549-Cre Et(REx2-SCP1:BGi-Cre)y549, N = 5; y550-Cre Et(REx2-SCP1:BGi-Cre)y550, N = 4; y551-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y551, N = 4; y552-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y552, N = 4. Image stacks are compressed nifti files (8 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).y553-y558This archive contains: y553-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y553, N = 6 larval zebrafish; y554-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y554, N = 4; y555-Cre Et(REx2-SCP1:BGi-Cre)y555, N = 3; y556-Cre Et(REx2-SCP1:BGi-Cre)y556, N = 4; y557-Cre Et(REx2-SCP1:BGi-Cre)y557, N = 5, y558-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y558, N = 4. Image stacks are compressed nifti files (y557 is 16 bit, others are 8 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).y559-y574This archive contains: y559-Cre Et(REx2-SCP1:BGi-Cre)y559, N = 4 larval zebrafish; y568-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y568, N = 6; y569-Cre Et(REx2-SCP1:BGi-Cre)y569, N = 7; y570-Cre Et(REx2-SCP1:BGi-Cre)y570, N = 5; y571-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y571, N = 8, y574-Cre Et(REx2-SCP1:BGi-Cre)y574, N = 4. Image stacks are compressed nifti files (8 bit), labeled as: "line identifier" - "fish #" - "color channel #". Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).