| Biological samples |
|
|
| Adult mouse olfactory bulb |
This study |
N/A |
| Adult mouse parabrachial nucleus |
This study |
N/A |
|
|
|
| Chemicals, peptides, and recombinant proteins |
| Contrad 70 |
Decon Labs |
Cat#1003 |
| 10N sodium hydroxide solution |
Sigma-Aldrich |
Cat#72068 |
| Hydrochloric acid |
Fisher Scientific |
Cat#A144-500 |
| 200 proof ethanol |
Decon Labs |
Cat#2701 |
| 3-(trimethoxysilyl)propyl methacrylate (Blind-Silane) |
Sigma-Aldrich |
Cat#M6514 |
| Acetic acid |
Fisher Scientific |
Cat#A35-500 |
| Acrylamide |
Sigma-Aldrich |
Cat#A9099 |
| N,N’-methylenebisacrylamide |
Sigma-Aldrich |
Cat#M7279 |
| Ammonium persulfate |
Sigma-Aldrich |
Cat#A3678 |
| UltraPure TEMED |
Invitrogen |
Cat#15524-010 |
| N-(5-bromoacetamidylpentyl) acrylamide (BRAPA) |
Combi-blocks |
Cat#HD-8626 |
| N, N-dimethylformamide |
Sigma-Aldrich |
Cat#D4551 |
| Potassium phosphate dibasic trihydrate |
Sigma-Aldrich |
Cat#P9666 |
| Potassium phosphate monobasic |
Sigma-Aldrich |
Cat#P9791 |
| 20× SSC |
Invitrogen |
Cat#AM9763 |
| Tween-20 |
Sigma-Aldrich |
Cat#P9416 |
| Taq2× master mix |
New England Biolabs |
Cat#M0270 |
| Trizma base |
Sigma-Aldrich |
Cat#93362 |
| Betaine |
Sigma-Aldrich |
Cat#B2629 |
| Ammonium sulfate |
Sigma-Aldrich |
Cat#A4418 |
| Magnesium sulfate |
Sigma-Aldrich |
Cat#M2773 |
| Triton X-100 |
Sigma-Aldrich |
Cat#T8787 |
| Dimethyl sulfoxide |
Sigma-Aldrich |
Cat#D8418 |
|
Taq DNA polymerase |
New England Biolabs |
Cat#M0267X |
| dNTP mix (10 mM each) |
GenScript |
Cat#C01582-250 |
| Formamide (deionized) |
Emdmillipore |
Cat#4670-4L |
|
Bst enzyme |
New England Biolabs (or This study) |
Cat#M0275 |
| USER enzyme |
New England Biolabs |
Cat#M5505 |
|
TaqI-V2 |
New England Biolabs |
Cat#R0149 |
| Maxima H minus reverse transcriptase |
Thermo Fisher Scientific |
Cat#EP0753 |
| O.C.T. compound |
Fisher Healthcare |
Cat#4585 |
| RNase inhibitor |
Invitrogen |
Cat#10777019 |
| Ficoll PM 400 |
Sigma-Aldrich |
Cat# F4375 |
| Proteinase K |
Qiagen |
Cat#19131 |
| PKD buffer |
Qiagen |
Cat#1034963 |
| BSA |
New England Biolabs |
Cat#M9000S |
|
Bst 2.0 WarmStart DNA polymerase |
New England Biolabs |
Cat#M0538L |
| Ultra II Q5 master mix |
New England Biolabs |
Cat#M0544L |
| Thermolabile exonuclease I |
New England Biolabs |
Cat#M0568L |
| Q5 HotStart polymerase |
New England Biolabs |
Cat#M0493L |
|
|
|
| Critical commercial assays |
| Nextera XT kit |
Illumina |
Cat#FC-131-1024 |
| HiSeq SBS kit v4 |
Illumina |
Cat#FC-401-4002 |
| RNAScope HiPlex assay |
ACDBio |
Cat#324409 |
| PhiX control library |
Illumina |
Cat#FC-110-3001 |
|
|
|
| Deposited data |
| Pixel-seq mouse OB and PBN data |
GEO |
GEO: GSE186097
|
| HDST mouse OB data |
GEO |
GEO: GSE130682
|
| Seq-scope mouse liver data |
GEO |
GEO: GES169706 |
| DBiT-seq mouse embryo data |
GEO |
GEO: GSE137986
|
| Slide-seqV2 mouse OB data |
Broad |
Stickels et al., 2021
|
| Visium mouse OB data |
GEO |
GEO: GSE153859
|
| scRNA-seq mouse OB data |
GEO |
GEO: GSE121891
|
| Stereo-seq mouse OB data |
CNGB |
CNGB:CNP0001543 |
|
|
|
| Oligonucleotides |
| BA(+): AATGATACGGCGACCACCGAGAUCTACAC |
Integrated DNA Technologies |
N/A |
| BA(−): CAAGCAGAAGACGGCATACGAGAT |
Integrated DNA Technologies |
N/A |
| PS-BA(+): /5PS/TTTTTTTTTTAATGATACGGCGACCACCGAGAUCTACAC |
Integrated DNA Technologies |
N/A |
| PS-BA(−): /5PS/TTTTTTTTTTCAAGCAGAAGACGGCATACGAGAT |
Integrated DNA Technologies |
N/A |
| Cy5-probe: /5Cy5/CTTGCGCTAGTCCGGCAACCTCGGTGG |
Integrated DNA Technologies |
N/A |
| UMI primer: CTACACGACGCTCTTCCGATCTNNNNNNNCCGCTAATACGACTCACTATAGGG |
Integrated DNA Technologies |
N/A |
| TruSeq sequencing primer: CCTACACGACGCTCTTCCGATC |
Integrated DNA Technologies |
N/A |
| TSO primer: /5’BIOSG/AAGCAGTGGTATCAACGCAGAGT |
Integrated DNA Technologies |
N/A |
| TruSeq libP5 primer: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT |
Integrated DNA Technologies |
N/A |
| Nextra index primer: CAAGCAGAAGACGGCATACGAGAT[INDEX]GTCTCGTGGGCTCGG |
Integrated DNA Technologies |
N/A |
| Polony sequencing primer: TTCCATCATTGTTCCCGGGTTCCTCATTCTC |
Integrated DNA Technologies |
N/A |
| Template-switching oligo: AAGCTGGTATCAACGCAGAGTGAATrG+GrG |
Qiagen |
339414YCO0076714 |
|
|
|
| Software and algorithms |
| STAR |
https://github.com/alexdobin/STAR
|
V2.7.0 |
| Cellpose |
https://www.cellpose.org/
|
V1.0 |
| Seurat |
https://satijalab.org/seurat/
|
V4.0.2 |
| iGraph |
https://igraph.org/
|
V1.3.0 |
| Flexbar |
https://github.com/seqan/flexbar
|
V3.0 |
| Bowtie |
http://bowtie-bio.sourceforge.net/
|
V1.3.1 |
| DA-seq |
https://github.com/KlugerLab/DAseq
|
V1.0.0 |
| Giotto |
https://rubd.github.io/Giotto_site/
|
V1.0.4 |
| Slingshot |
https://github.com/kstreet13/slingshot
|
V2.2.0 |
| SpaOTsc |
https://github.com/zcang/SpaOTsc
|
V1.0 |
| Dlight |
https://github.com/GuLABatUW/Pixel-seq/tree/main/BaseCalling_DlightV2.3
|
V2.3 |
| Micro-Manager |
https://www.micro-manager.org
|
V1.4.22 |
| jSerialComm |
http://fazecast.github.io/jSerialComm/
|
N/A |
|
|
|
|
|
|
| Other |
| 4-axis robotic arm |
DOBOT |
Model: MG400 |
| CPAC HT 2-TEC Heating/cooling block |
Inheco |
PN:7000166 |
