| Genetic reagent (Gallus gallus) |
GRCg6a |
International Chicken Genome Consortium |
GCF_000002315.5 |
|
| Species |
Fertilized chicken eggs (specific pathogen free) |
Charles River Laboratories |
Cat# 10100326 |
|
| Sequenced-based reagent |
Sequences of probes used for in situ hybridization |
IDT |
Supplementary file 1 in this study |
|
| Sequenced-based reagent |
Sequences of homology arms used to generate eCHIKIN probes |
IDT, this study |
Supplementary file 2 in this study |
|
| Sequenced-based reagent |
Alt-R CRISPR-Cas9 crRNA (specific to each gene) |
IDT |
Supplementary file 2 in this study |
|
| Recombinant DNA reagent |
pXL-BacII-CAG-Zeocin-3xF2A |
Martell et al., 2016 (doi:10.1038/nbt.3563) |
|
|
| Recombinant DNA reagent |
pCAG-PBorf |
Yamagata and Sanes, 2012 (doi:10.1523/JNEUROSCI.3193-12.2012) |
|
|
| Recombinant DNA reagent |
pXL-BacII-CAG-mCherry |
This study |
|
|
| Recombinant DNA reagent |
pXL-BacII--loxP-STOP-loxP-Venus |
This study |
|
|
| Recombinant DNA reagent |
pXL-BacII-CAG-Venus |
Yamagata and Sanes, 2012 (doi:10.1523/JNEUROSCI.3193-12.2012) |
|
|
| Recombinant DNA reagent |
pCAG-Cre:GFP |
Addgene |
Addgene#13776 |
|
| Antibody |
Anti-chicken Thy1 (Mouse monoclonal) |
BSJ-1 (French and Jeffrey, 1986, doi:10.1002/jnr.490160304) |
|
0.01 µ /ml for cell purification |
| Antibody |
Anti-Calbindin (Rabbit polyclonal) |
Swant |
Cat# CB-38a; RRID:AB_10000340
|
IF(1/1000) |
| Antibody |
Anti-GFP (Rabbit polyclonal) |
Millipore |
Cat# AB3080P; RRID:AB_2630379
|
IF(1/1000) |
| Antibody |
Anti-Brn3a (Mouse monoclonal) |
Millipore |
Cat# MAB1585; RRID:AB_94166
|
IF(1/1000) |
| Antibody |
Anti-Calretinin (Rabbit polyclonal) |
Millipore |
Cat# AB5054; |
IF(1/1000) |
| RRID:AB_2068506
|
| Antibody |
Anti-Calbindin (Rabbit polyclonal) |
Swant |
Cat# CB38; RRID:AB_10000340
|
IF(1/1000) |
| Antibody |
Anti-Protein kinase C- α (Rabbit polyclonal) |
Sigma |
Cat# P4334 |
IF(1/10000) |
| Antibody |
Anti-VSX2 (Rabbit polyclonal) |
GeneTex |
Cat# GTX114143 |
IF(1/1000) |
| Antibody |
Anti-HA tag (Rat monoclonal) |
Roche |
Clone name: 3F10 |
IF(1/1000) |
| Antibody |
Anti-Satb1 (Rabbit polyclonal) |
Abcam |
Cat# ab109122; RRID:AB_10862207
|
IF(1/1000) |
| Antibody |
Anti-Satb2 (Mouse monoclonal) |
Abcam |
Cat# ab51502; RRID:AB_882455
|
IF(1/1000) |
| Antibody |
Anti-Neuropeptide Y (Rabbit polyclonal) |
Abcam |
Cat# ab10980 |
IF(1/1000) |
| Antibody |
Anti-AP2A (Mouse monoclonal) |
Developmental Studies Hybridoma Bank |
Clone name: 3B5 |
IF(1/100) |
| Antibody |
Anti-AP2B (Mouse monoclonal) |
Developmental Studies Hybridoma Bank |
Clone name: 2A4 |
IF(1/100) |
| Antibody |
Anti-OTX1 (Mouse monoclonal) |
Developmental Studies Hybridoma Bank |
Clone name: 5F5 |
IF(1/100) |
| Antibody |
Anti-SOX5 (Mouse monoclonal) |
Developmental Studies Hybridoma Bank |
Clone name: 1C12 |
IF(1/100) |
| Antibody |
Anti-PAX6 (Mouse monoclonal) |
Developmental Studies Hybridoma Bank |
Clone name: PAX6 |
IF(1/100) |
| Antibody |
Anti-NMB (Mouse monoclonal) |
Developmental Studies Hybridoma Bank |
Clone name: NMB1 |
IF(1/10) |
| Antibody |
Anti-STRA6 (Mouse polyclonal) |
This study |
|
IF (1:1000) |
| Antibody |
Anti-TPBGL (Mouse polyclonal) |
This study |
|
IF (1:500) |
| Antibody |
Anti-SLC6A4 (Mouse polyclonal) |
This study |
|
IF (1:200) |
| Antibody |
Anti-chicken choline acetyltransferase (Rabbit polyclonal) |
Johnson and Epstein, 1986 (doi:10.1111/j.1471-4159.1986.tb13064.x) |
|
IF (1:1000) |
| Antibody |
Anti-chicken glutamate synthetase (Rabbit polyclonal) |
Linser and Moscona, 1979 (doi: 10.1073/pnas.76.12.6476) |
|
IF (1:1000) |
| Commercial assay or kit |
Papain Dissociation System, Without EBSS |
Worthington |
Cat# LK003160
|
|
| Commercial assay or kit |
Chromium Single Cell 30Library and Gel Bead Kit v2, 10X Genomics Cat#120237 16rxns |
10 X Genomics |
Cat# 120237 |
|
| Chemical compound, drug |
Goat anti-mouse IgG conjugated magnetic beads |
Miltenyi Biotec |
Cat# 484–02 |
|
| Chemical compound, drug |
Alt-R CRISPR-Cas9 tracrRNA |
IDT |
Cat# 1072533 |
|
| Chemical compound, drug |
Alt-R S.p. Cas9 Nuclease V3 |
IDT |
Cat# 1081058 |
|
| Chemical compound, drug |
Alt-R Cas9 Electroporation Enhancer |
IDT |
Cat# 1075915 |
|
| Chemical compound, drug |
Alt-R HDR Enhancer |
IDT |
Cat# 1081072 |
|
| Chemical compound, drug |
Fast Green FCF |
Sigma-Aldrich |
Cat# F7252 |
|
| Commercial assay or kit |
TSA Cyanine 3 Plus Evaluation Kit |
Perkin Elmer |
Cat# NEL744E001KT (FP1170) |
|
| Commercial assay or kit |
TSA Fluorescein Plus Evaluation Kit |
Perkin Elmer |
Cat# NEL741E001KT (FP1168) |
|
| Chemical compound, drug |
Anti-Digoxigenin-POD, Fab fragments |
Roche |
Cat# 11207733910 |
|
| Commercial assay or kit |
EconoTaq PLUS GREEN 2X Master Mix |
Lucigen |
Cat# 30033–1 |
|
| Commercial assay or kit |
CIAquick-Gel Extraction Kit |
Oiagen |
Cat# 28704 |
|
| Commercial assay or kit |
MiniMACS Separation Unit |
Miltenyi Biotec |
Cat# 421–02 |
|
| Other |
MACS Multistand |
Miltenyi Biotec |
Cat# 423–03 |
|
| Other |
Type WHM large cell separation columns |
Miltenyi Biotec |
Cat# 422–02 |
|
| Other |
BTX 830 |
BTX |
Cat# 45–0662 |
|
| Other |
Genetrode |
BTX |
Cat# 45–0116 |
|
| Software, algorithm |
ImageJ (Fiji) Version 2.1.0 |
Fiji |
https://imagej.net/Fiji |
|
| Software, algorithm |
R 3.6.2 |
The R foundation |
https://www.r-project.org/ |
|
| Software, algorithm |
RStudio 1.3.1056 |
Rstudio |
https://rstudio.com |
|
| Software, algorithm |
Adobe Photoshop 20.0.9 release |
Adobe |
https://www.adobe.com |
|
