| Antibodies |
| Anti-chicken Green Fluorescent Protein Antibody |
Aves Labs |
Cat #: GFP-1010 RRID:AB_2307313 |
| Anti-rabbit Green Fluorescent Protein Antibody |
Thermo Fisher |
Cat #: A11122 RRID:AB_221569 |
| Anti-chicken mCherry Antibody |
Abcam |
Cat #: ab205402 RRID:AB_2722769 |
| Anti-rat CD68 Antibody |
BioRad |
Cat #: MCA1957 RRID:AB_322219 |
| Anti-rabbit IBA1 Antibody |
Abcam |
Cat #: ab178847 RRID:AB_2832244 |
| Anti-rabbit IBA1 Antibody |
Wako Chemicals |
Cat #: 01919741 RRID:AB_839504 |
| Anti-goat IBA1 Antibody |
Invitrogen |
Cat #: PA518039 RRID:AB_10982846 |
| Anti-rat CD31 Antibody |
BD Biosciences |
Cat #: BDB550274 RRID:AB_393571 |
| Anti-goat CD31 Antibody |
R&D Systems |
Cat #: AF3628 RRID:AB_2161028 |
| Anti-goat mAxl Antibody |
R&D Systems |
Cat #:AF854 RRID:AB_355663 |
| Anti-mouse Tenascin C Antibody |
Novus Biologicals |
Cat #: NB11068136 RRID:AB_1110904 |
| Anti-rabbit Tenascin C Antibody |
Millipore |
Cat #: AB19011 RRID:AB_2203804 |
| Anti-rabbit Collagen type IV Antibody |
Serotec |
Cat #: 21501470 RRID:AB_2082660 |
| Anti-rabbit Periostin Antibody |
Thermo Fisher |
Cat #: PA582458 RRID:AB_278916 |
| Anti-mouse Fibronectin Antibody |
Thermo Fisher |
Cat #: MIF2601 RRID:AB_11154171 |
| Anti-rat GFAP Antibody |
Thermo Fisher |
Cat #: 130300 RRID:AB_2532994 |
| Anti-rat BrdU Antibody |
Abcam |
Cat #: ab6326 RRID:AB_305426 |
| Alexa-Fluor 488 Donkey anti-Chicken |
Jackson ImmunoResearch |
Cat #: 703545155 RRID:AB_2340375 |
| Alexa-Fluor 488 Donkey anti-Goat |
Thermo Fisher |
Cat #: A32814 RRID:AB_2762838 |
| Alexa-Fluor 546 Donkey anti-Goat |
Thermo Fisher |
Cat #: A11056 RRID:AB_2534103 |
| Alexa-Fluor 546 Donkey anti-Mouse |
Thermo Fisher |
Cat #: A10036 RRID:AB_2534012 |
| Alexa-Fluor 568 Donkey anti-Rabbit |
Thermo Fisher |
Cat #: A10042 RRID:AB_2534017 |
| Alexa-Fluor 647 Donkey anti-Chicken |
Jackson ImmunoResearch |
Cat #: 703605155 RRID:AB_2340379 |
| Alexa-Fluor 647 Donkey anti-Rat |
Thermo Fisher |
Cat #: A48272 RRID:AB_2893138 |
| Alexa-Fluor 647 Donkey anti-Rabbit |
Thermo Fisher |
Cat #: A31573 RRID:AB_2538183 |
| Alexa-Fluor 750 Donkey anti-Goat |
Abcam |
Cat #: ab175745 RRID:AB_2924800 |
| Alexa-Fluor 750 Donkey anti-Rabbit |
Abcam |
Cat #: ab175728 RRID:AB_2924801 |
| Human TruStain FcX (Fc receptor blocking solution) |
BioLegend |
Cat #: 422301 RRID:AB_2818986 |
| Anti-mouse CD16/32 |
BioLegend |
Cat #: 101319 RRID:AB_1574973 |
| TotalSeq-A0253 anti-human Hashtag 3 Antibody |
BioLegend |
Cat #: 394605 RRID:AB_2750017 |
| TotalSeq-A0255 anti-human Hashtag 5 Antibody |
BioLegend |
Cat #: 394609 RRID:AB_2750019 |
| TotalSeq-A0256 anti-human Hashtag 6 Antibody |
BioLegend |
Cat #: 394611 RRID:AB_2750020 |
| TotalSeq-A0258 anti-human Hashtag 8 Antibody |
BioLegend |
Cat #: 394615 RRID:AB_2750022 |
| TotalSeq-A0306 anti-mouse Hashtag 6 Antibody |
BioLegend |
Cat #: 155811 RRID:AB_2750037 |
| TotalSeq-A0307 anti-mouse Hashtag 7 Antibody |
BioLegend |
Cat #: 155813 RRID:AB_2750039 |
| TotalSeq-A0308 anti-mouse Hashtag 8 Antibody |
BioLegend |
Cat #: 155815 RRID:AB_2750040 |
| FITC Annexin V |
BioLegend |
Cat #: 649020 |
| Bacterial and virus strains |
|
Stbl3 competent E. coli
|
ThermoFisher |
Cat #: C737303 |
|
endA competent E. coli
|
New England Biolabs |
Cat #: C3040H |
| Biological samples |
| Brain metastasis tissue samples derived from TNBC patients (n = 13) and HER2BC patients (n = 18) |
Department of Pathology, MSKCC |
|
| Chemicals, peptides, and recombinant proteins |
| Dulbecco’s Modified Eagle’s high glucose medium |
Media Preparation Core, MSKCC |
Powder Cat #: 52100047 |
| Dulbecco’s Phosphate-Buffered Saline, no calcium, no magnesium |
Media Preparation Core, MSKCC |
Powder Cat #: 21600044 |
| Roswell Park Memorial Institute 1640 medium |
Media Preparation Core, MSKCC |
Powder Cat #: 31800105 |
| Fetal Bovine Serum |
Sigma Aldrich |
Cat #: F2442 |
| L-glutamine |
Thermo Fisher |
Cat #: 25030081 |
| Penicillin-Streptomycin |
Thermo Fisher |
Cat #: 15140163 |
| Amphotericin B |
Gemini Bio-Products |
Cat #: 400104 |
| DiD’ solid; DiIC18(5) solid (1,1’-Dioctadecyl-3,3,3’,3’-Tetramethylindodicarbocyanine, 4-Chlorobenzenesulfonate Salt) |
Thermo Fisher |
Cat #: D7757 |
| B-27 Supplement, serum free |
Thermo Fisher |
Cat #: 17504001 |
| Human Recombinant bFGF, ACF |
StemCell Technologies |
Cat #: 02634 |
| Human EGF Recombinant Protein |
Thermo Fisher |
Cat #: PHG0311 |
| D-luciferin, Potassium Salt |
GoldBio |
Cat #: LUCK-10G |
| Heparin sodium salt |
Sigma Aldrich |
Cat #: H3393 |
| Paraformaldehyde Aqueous Solution |
Electron Microscopy Sciences |
Cat #: 15710S |
| Tissue-Tek O.C.T Compound |
Sakura |
Cat #: 4583 |
| Isoflurane Solution |
Covetrus |
Cat #: 029405 |
| Sucrose |
Fisher Scientific |
Cat #: S53 |
| Polyethylene glycol |
Millipore Sigma |
Cat #: 8170025000 |
| Glycerol |
Thermo Fisher |
Cat #: BP2291 |
| β-Mercaptoethanol |
Sigma Aldrich |
Cat #: M3148100ML |
| Lipofectamine 2000 |
Thermo Fisher |
Cat #: 11668019 |
| Opti-MEM |
Thermo Fisher |
Cat #: 31985062 |
| Lenti-X Concentrator |
Clontech |
Cat #: 631231 |
| Polybrene |
Santa Cruz Biotechnology |
Cat #: sc134220 |
| G 418 disulfate salt solution |
Thermo Fisher |
Cat #: 10131035 |
| Puromycin dihydrochloride |
Sigma Aldrich |
Cat #: P962010ML |
| Actinomycin D |
Sigma Aldrich |
Cat #: A1410 |
| Triptolide |
Sigma Aldrich |
Cat #: T3652 |
| Anisomycin from Streptomyces griseolus
|
Sigma Aldrich |
Cat #: A9789 |
| 5-Fluorocytosine |
Sigma Aldrich |
Cat #: F71291G |
| SeaPlaque Agarose |
Lonza |
Cat #: 50100 |
| BsmBI-v2 |
New England Biolabs |
Cat #: R07395
|
| CellTrace Calcein Violet, AM, for 405 nm |
Thermo Fisher |
Cat #: C34858
|
| DAPI (4’,6-Diamidino-2-Phenylindole Dilactate) |
Thermo Fisher |
Cat #: D3571 |
| Critical commercial assays |
| RNeasy Mini Kit |
QIAgen |
Cat #: 74106 |
| QIAshredder |
QIAgen |
Cat #: 76956 |
| Transcriptor First Strand cDNA Synthesis Kit |
Roche |
Cat #: 04897030001 |
| SMARTer PCR cDNA Synthesis Kit |
Clontech |
Cat #: 634926 |
| TruSeq RNA Sample Prep Kit v2 |
Illumina |
Cat #: RS1222001 |
| NEBNext Ultra RNA Library Prep Kit |
New England Biolabs |
Cat #: E7530S |
| Adult Brain Dissociation Kit |
Miltenyi Biotec |
Cat #: 130107677 |
| Dead Cell Removal Kit |
Miltenyi Biotec |
Cat #: 130090101 |
| Deposited data |
| Patient Survival Datasets |
Györffy et al. |
PMID: 20020197 |
| Lanczky et al. |
PMID: 27744485 |
| Microarray Gene Expression Data |
Bos et al. |
GEO: GSE12237
|
| Atlas of the Adolescent Mouse Brain |
Zeisel et al. |
mousebrain.org
|
| DepMap |
Broad Institute |
depmap.org/portal/
|
| MetMap |
Jin et al. |
GEO: GSE148283, GSE148372
|
| Raw and processed data files for RNA-seq |
This study |
GEO: GSE223351
|
| Raw and processed data files for Flura-seq |
This study |
GEO: GSE223247
|
| Raw and processed data files for single-cell RNA-seq |
This study |
GEO: GSE223309
|
| Experimental models: Cell lines |
| HEK293T |
ATCC |
ATCC #: CRL-3216 |
| E0771-BrM |
Derived in house |
This paper |
| MDA231-BrM |
Derived in house |
This paper |
| HCC1954-BrM |
Derived in house |
This paper |
| MMTV-ErbB2-BrM |
Derived in house |
This paper |
| Experimental models: Organisms/strains |
| Mouse: Hsd:Athymic Nude-Fox1nu
|
ENVIGO |
Order code: 069 |
| Mouse: B6(Cg)-Tyrc-2J/J (B6 albino) |
The Jackson Laboratory |
Strain #: 000058 RRID: IMSR_JAX:000058 |
| Mouse: FVB/NJ |
The Jackson Laboratory |
Strain #: 001800 RRID: IMSR_JAX:001800 |
| Oligonucleotides |
| TaqMan human TNC (Hs01115665_m1) |
Thermo Fisher |
Cat #: 4453320 |
| TaqMan human GAS6 (Hs01090305_m1) |
Thermo Fisher |
Cat #: 4331182 |
| TaqMan human COL4A1 (Hs00266237_m1) |
Thermo Fisher |
Cat #: 4453320 |
| TaqMan human GAPDH (Hs02786624_g1) |
Thermo Fisher |
Cat #: 4331182 |
| TaqMan human ACTB (Hs01060665_g1) |
Thermo Fisher |
Cat #: 4331182 |
| TaqMan human AXL (Hs01064444_m1) |
Thermo Fisher |
Cat #: 4453320 |
| TaqMan mouse Tnc (Mm00495662_m1) |
Thermo Fisher |
Cat #: 4453320 |
| TaqMan mouse Gas6 (Mm00490378_m1) |
Thermo Fisher |
Cat #: 4453320 |
| TaqMan mouse Col4a1 (Mm01210125_m1) |
Thermo Fisher |
Cat #: 4453320 |
| TaqMan mouse Gapdh (Mm99999915_g1) |
Thermo Fisher |
Cat #: 4331182 |
| TaqMan mouse ActB (Mm0120567_g1) |
Thermo Fisher |
Cat #: 4453320 |
| TaqMan mouse Axl (Mm00437221_m1) |
Thermo Fisher |
Cat #: 4453320 |
| 97-mer oligonucleotide containing shTNC 1: TGCTGTTGACAGTGAGCGACAGAGGTGACATGTCAAGCAATAGTGAAGCCACAGATGTATTGCTTGACATGTCACCTCTGCTGCCTACTGCCTCGGA |
This paper |
Synthesized by IDT |
| 97-mer oligonucleotide containing shTNC 2: TGCTGTTGACAGTGAGCGACAGCTATTGACAGTTACAGAATAGTGAAGCCACAGATGTATTCTGTAACTGTCAATAGCTGCTGCCTACTGCCTCGGA |
This paper |
Synthesized by IDT |
| 97-mer oligonucleotide containing shCOL4A1 1: TGCTGTTGACAGTGAGCGCCCAGGACAAGCTCAAGTTCAATAGTGAAGCCACAGATGTATTGAACTTGAGCTTGTCCTGGTTGCCTACTGCCTCGGA |
This paper |
Synthesized by IDT |
| 97-mer oligonucleotide containing shCOL4A1 2: TGCTGTTGACAGTGAGCGCCCCGGAAAAGATGGTGACAAATAGTGAAGCCACAGATGTATTTGTCACCATCTTTTCCGGGTTGCCTACTGCCTCGGA |
This paper |
Synthesized by IDT |
| 97-mer oligonucleotide containing shAXL 1: TGCTGTTGACAGTGAGCGAAAAGTCTCTAATTCTATTAAATAGTGAAGCCACAGATGTATTTAATAGAATTAGAGACTTTGTGCCTACTGCCTCGGA |
This paper |
Synthesized by IDT |
| 97-mer oligonucleotide containing shAXL 2: TGCTGTTGACAGTGAGCGCCCAAAGTCTCTAATTCTATTATAGTGAAGCCACAGATGTATAATAGAATTAGAGACTTTGGATGCCTACTGCCTCGGA |
This paper |
Synthesized by IDT |
| 97-mer oligonucleotide containing shGAS6 1: TGCTGTTGACAGTGAGCGCCCAGGAAACGGTGAAAGTGAATAGTGAAGCCACAGATGTATTCACTTTCACCGTTTCCTGGATGCCTACTGCCTCGGA |
This paper |
Synthesized by IDT |
| 97-mer oligonucleotide containing shGAS6 2: TGCTGTTGACAGTGAGCGAAGCGAGGACTGTATCATCTGATAGTGAAGCCACAGATGTATCAGATGATACAGTCCTCGCTCTGCCTACTGCCTCGGA |
This paper |
Synthesized by IDT |
| Oligonucleotides for Tnc sgRNA 1: |
This paper |
Synthesized by IDT |
| Sense: CACCGCACACACCCTAGCCTCTGGT |
| Antisense: AAACACCAGAGGCTAGGGTGTGTGC |
| Oligonucleotides Tnc sgRNA 2: |
This paper |
Synthesized by IDT |
| Sense: CACCGACACACACCCTAGCCTCTGG |
| Antisense: AAACCCAGAGGCTAGGGTGTGTGTC |
| Oligonucleotides for Col4a1 sgRNA 1: |
This paper |
Synthesized by IDT |
| Sense: CACCGCGAGGTGCTCAGTCTCGGA |
| Antisense: AAACTCCGAGACTGAGCACCTCGC |
| Oligonucleotides for Col4a1 sgRNA: |
This paper |
Synthesized by IDT |
| Sense: CACCGGCGAGGTGCTCAGTCTCGG |
| Antisense: AAACCCGAGACTGAGCACCTCGCC |
| Oligonucleotides for Gal4 sgRNA: |
This paper |
Synthesized by IDT |
| Sense: CACCGAACGACTAGTTAGGCGTGTA |
| Antisense: AAACTACACGCCTAACTAGTCGTTC |
| Recombinant DNA |
| Plasmid: HSV1-TK/GFP/Fluc/ |
Ponomarev et al. |
|
| Plasmid: pLV[Exp]-BsdEF1A>hGAS6[NM_000820.4] |
Vector Builder |
Cat #: Ecoli(VB900126-3640pet) |
| Plasmid: pLV[Exp]-Bsd-EF1A>ORF_Stuffer |
Vector Builder |
Cat #: Ecoli(VB900122-0480ezn) |
| Plasmid: sLP-mCherry-P2A-eGFP |
Tammela Lab |
|
| Plasmid: IGI-P0492 pHR-dCas9-NLS-VPR-mCherry |
Jacob Corn Lab |
Addgene #102245 |
| Plasmid: dCas9-KRAB-MECP2 |
Yeo et al. |
Addgene #110821 |
| Plasmid: lentiGuide-Hygro-mTagBFP2 |
Ho et al. |
Addgene #99374 |
| Plasmid: SGEN |
Fellmann et al. |
Addgene #111171 |
| Plasmid: LENC |
Fellmann et al. |
Addgene #111163 |
| Plasmid: LEPZ |
Fellmann et al. |
Addgene #111161 |
| Software and algorithms |
| Living Image |
PerkinElmer |
Version 4.4 |
| ImageJ |
NIH |
Version 2 |
| FIJI |
NIH |
Version 2.3.0/1.53q |
| Imaris |
Oxford Instruments Group |
Version 9.5.0 |
| STAR RNA-seq aligner |
Dobin et al. |
Version 2.5.3a |
| HTSeq |
Anders et al. |
Version 0.6.1p1 |
| DESeq2 |
Bioconductor |
Version 3.4.1 |
| Xenome |
Conway et al. |
Version 1.0.1 |
| DAVID |
Huang et al. |
Version 6.8 |
| RStudio |
RStudio |
Version 1.2.5029 |
| Prism |
GraphPad |
Version 8.4.3 |
| SEQC |
https://github.com/dpeerlab/seqc
|
Version 0.2.1 |
| Scanpy |
Wolf et al. |
Version 1.6.0 |
| Python |
Python |
Version 3.8.5 |
| CellBender |
Fleming et al. |
Version 0.2.0 |
| DropletUtils |
Lun et al. |
Version 1.10.3 |
| SHARP |
https://github.com/hisplan/sharp
|
Version 0.2.1 |
| DoubletDetection |
https://github.com/dpeerlab/DoubletDetection
|
Version 2.5.2 |
| PhenoGraph |
Levine et al. |
Version 1.5.6 |
| Milo |
Dann et al. |
Version 0.1.0 |
| EdgeR |
Chen et al. |
Version 3.32.1 |
| MAST |
Finak et al. |
Version 1.16.0 |
| GSEA |
Mootha et al. |
Version 4.0.3 |
| scran |
Lun et al. |
Version 1.14.6 |
| Palantir |
Setty et al. |
Version 1.1 |
| Other |
| Clamp Lamp Light with 8.5 Inch Aluminum Reflector |
Simple Deluxe |
Cat #: B08MZKQNP4 |
| 250W clear bulb |
VWR |
Cat #: 36548001 |
| ProLong Diamond Antifade mountant |
Thermo Fisher |
Cat #: P36961
|
| VWR Slides Micro Frosted |
VWR |
Cat #: 48312-003 |
| Fisherbrand Premium Cover Glasses |
Fisher Scientific |
Cat #: 125485M |
| Corning Falcon Standard Tissue Culture Dishes |
Fisher Scientific |
Cat #: 08772E |
| Corning Costar Ultra-Low Attachment Microplates |
Corning |
Cat #: 07200601 |
| Single-use Syringe/BD PrecisioGlide Needle |
VWR |
Cat #: BD309625
|
| Myelin Removal Beads II, human, mouse, rat |
Miltenyi Biotec |
Cat #: 130090101 |
| Oligo (dT)25 magnetic beads |
New England Biolabs |
Cat #: S1419S |
