Key Resources Table.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti CD326-Brillianat Violet 510 (EPCAM) | Biolegend | Cat#324235; PRID: AB_2632934 |
| Mouse monoclonal anti CD45- PE/Cy7 | Biolegend | Cat#368531; PRID: AB_2715891 |
| Mouse monoclonal anti alpha-Smooth Muscle Actin-APC | Novus Biologicals | Cat#NBP2-47698APC; PRID: N/A |
| Mouse monoclonal anti ENG (CD105)-PE | Abcam | Cat#ab53321; PRID: AB_868769 |
| Mouse monoclonal anti RUNX3-Alexa 488 | R&D Systems | Cat#IC3765G-100UG; PRID: N/A |
| Mouse monoclonal anti mouse IgG2b, κ isotype control antibody-Brilliant Violet 510 | Biolegend | Cat#400345; PRID: N/A |
| Mouse monoclonal anti mouse IgG2a, κ isotype control antibody-Alexa 488 | Biolegend | Cat#400233; PRID: N/A |
| Rat monoclonal anti mouse IgG2a antibody-APC | Biolegend | Cat#407109; PRID: AB_2561754 |
| Mouse monoclonal anti mouse IgG1, κ isotype control antibody-PE/Cy7 | Biolegend | Cat#400126; PRID: AB_326448 |
| Mouse monoclonal anti mouse IgG2a, κ isotype control (FC) antibody-PE | Biolegend | Cat#400213; PRID: AB_2800438 |
| Mouse monoclonal anti FOXJ1 | Invitrogen | Cat#14-9965-82; PRID: AB_1548835 |
| Mouse monoclonal anti FOXJ1 | Sigma | Cat#AMAB91254; PRID: AB_2665866 |
| Rabbit polyclonal anti PAX8 | Proteintech | Cat#10336-1-AP; PRID: AB_2236705 |
| Rabbit monoclonal anti PAX8 | Abcam | Cat#ab239363; PRID: N/A |
| Rabbit monoclonal anti EPCAM-Alexa 488 | Abcam | Cat#ab237395; PRID: N/A |
| Rabbit polyclonal anti CAPS | Sigma | Cat#HPA043520; PRID: AB_10964138 |
| Mouse monoclonal anti alpha-Smooth Muscle Actin (ACTA2)-594 | Abcam | Cat#ab202368; PRID: N/A |
| Rabbit polyclonal anti CAVIN 2 (SDPR) | Proteintech | Cat#12339-1-AP; PRID: AB_2183305 |
| Rat monoclonal anti CD44 | Invitrogen | Cat#14-0441-82; PRID: AB_467246 |
| Mouse monoclonal anti Estrogen receptor 1 (ESR1) | Invitrogen | Cat#MA5-13191; PRID: AB_10986080 |
| Rabbit polyclonal anti Progesterone receptor (PGR) | Sigma | Cat#HPA008428; PRID: AB_1079680 |
| Rabbit polyclonal anti RUNX3 | Sigma | Cat#HPA059006; PRID: AB_2683877 |
| Rabbit monoclonal anti CD34 | Abcam | Cat#ab81289; PRID: AB_1640331 |
| Rabbit polyclonal anti LGALS1 | Sigma | Cat#HPA000646; PRID: AB_1078935 |
| Rabbit monoclonal anti CDKN2A | Abcam | Cat#ab108349; PRID: AB_10858268 |
| Biological samples | ||
| Adult Human 1 (FT1, Age 52 yrs) Fallopian Tube Tissue For single cell RNAseq and statining |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 2 (FT2, Age 30 yrs) Fallopian Tube Tissue For single cell RNAseq |
International Institute for the Advancement of Medicine | N/A |
| Adult Human 3 (FT3, Age 46 yrs) Fallopian Tube Tissue For single cell RNAseq, staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 4 (FT4, Age 31 yrs) Fallopian Tube Tissue For single cell RNAseq |
International Institute for the Advancement of Medicine | N/A |
| Adult Human 5 (FT5, Age 34 yrs) Fallopian Tube Tissue For single cell RNAseq, staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 6 (FT6, Age 32 yrs) Fallopian Tube Tissue For single cell RNAseq |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 7 (Age 71 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 8 (Age 52 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 9 (Age 72 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 10 (Age 68 yrs) Fallopian TubeTissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 11 (Age 58 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 12 (Age 47 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 13 (Age 36 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 14 (Age 49 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 15 (Age 36 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 16 (Age 41 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Adult Human 17 (Age 38 yrs) Fallopian Tube Tissue For staining and quantification |
University of Michigan Michigan Medicine RSRSR | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Proteinase | Sigma | Cat#P5147-1G |
| Deoxyribonuclease I | Sigma | Cat#4716728001 |
| Collagenase D | Sigma/Roche | Cat#11088866001 |
| Hyalurondase | Sigma | Cat#H3884-1G |
| HBSS | Invitrogen | Cat#14025092 |
| DAPI | Sigma | Cat#D9542 |
| FBS | Sigma | Cat#F4135 |
| Vectashield Antifade Mounting Medium | Vector Laboratories | Cat#H-1000-10 |
| Tween-20 | Sigma | Cat# P1379 |
| Triton X-100 | Sigma | Cat# T8787 |
| BSA | Sigma | Cat# A7030 |
| Paraformaldehyde | MilliporeSigma | Cat# 818715 |
| Bloxall Endogenous Peroxidase and Alkaline Phosphatase Blocking Solution | Vector Laboratories | Cat# SP-6000 |
| Sucrose | Sigma | Cat# S9378 |
| Citric Acid | Sigma | Cat#791725 |
| SignalBoostImmunoreaction Enhancer Kit | MilliporeSigma | Cat#407207 |
| EasySep RBC Depletion Reagent | Stemcell Technologies | Cat#18170 |
| Bacto™ FA Buffer | BD Biosciences | Cat#223142 |
| Deposited data | ||
| Raw data files for scRNA-seq | This paper or NCBI Sequence Read Archive or Human Cell Atlas | SRA: SRP323939; HCA: https://data.humancellatlas.org/explore/projects/21ea8ddb-525f-4f1f-a820-31f0360399a2 |
| Gene expression data for scRNA-seq | This paper or NCBI Gene Expression Omnibus or Human Cell Atlas | GEO: GSE178101; HCA: https://data.humancellatlas.org/explore/projects/21ea8ddb-525f-4f1f-a820-31f0360399a2 |
| Data visualization for scRNA-seq | This paper or cellxgene | https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c |
| Deposited code | Zenodo or Github | DOI:10.5281/zenodo.5883840; https://github.com/qianqianshao/FallopianTube/ |
| Software and algorithms | ||
| Cell Ranger (v4.0.0) | https://github.com/10XGenomics/cellranger | |
| SoupX (v1.4.5) | Young and Behjati, 2020 | https://github.com/constantAmateur/SoupX |
| DoubletFinder (v2.0.3) | McGinnis et al., 2019 | https://github.com/chris-mcginnis-ucsf/DoubletFinder |
| Seurat (v3.2.3) | Satija et al., 2019 | https://github.com/satijalab/seurat |
| SeuratWrappers (v0.1.0) | https://github.com/satijalab/seurat-wrappers | |
| velocyto.py (v0.17.17) | Manno et at., 2018 | https://github.com/velocyto-team/velocyto.py |
| scVelo (v0.2.3) | Bergen et al., 2020 | https://github.com/theislab/scvelo |
| LRpath | Kim et al., 2012 | http://lrpath.ncibi.org/ |