| Antibodies |
|
|
|
| mCD25 |
BD Biosciences, BioLegend, Tonbo |
Clone PC61 |
| FoxP3 |
Invitrogen |
Clone FJK16S |
| mCD44 |
BD Biosciences, BioLegend, Tonbo |
Clone IM7 |
| mCD62L |
BioLegend, Tonbo |
Clone MEL-14 |
| mICOS |
BioLegend |
Clone 398.4A |
| Ki67 |
BD Biosciences |
Clone B56 |
| mCTLA-4 |
BioLegend |
Clone UC10–4B9 |
| mCD103 |
BD Biosciences |
Clone M290 |
| mNrp-1 |
BD Biosciences |
Clone 3E12 |
| mCD39 |
BioLegend |
Clone Duha 59 |
| mCD73 |
BioLegend |
Clone TY/11.8 |
| mTim-3 |
BioLegend |
Clone RMT 3–23 |
| mTim-3 |
R&D Systems |
Clone FAB1529 |
| Flag |
BioLegend |
Clone L5 |
| mPD-1 |
BioLegend |
Clone RMP1–30 |
| mIL-10 |
BioLegend |
Clone JES5–16E3 |
| mCD90.2 |
BD Biosciences, BioLegend |
Clone 532.1 |
| mCD45.2 |
BioLegend |
Clone 104 |
| Helios |
BioLegend |
Clone 22F6 |
| mKlrg-1 |
BioLegend |
Clone 2F1 |
| mLy6g |
Tonbo |
Clone IA8 |
| mGITR |
eBioscience |
Clone DTA-1 |
| mCD4 |
BD Biosciences, BioLegend, Tonbo |
Clone RM-4–5 |
| mTIGIT |
BioLegend |
Clone 1G9 |
| mLAG-3 |
Invitrogen |
Clone C9B7W |
| mGARP |
BioLegend |
Clone F011–5 |
| phospho-S6 |
BioLegend |
Clone A17020B |
| phospho-ERK |
BioLegend |
Clone 4B11B69 |
| phospho-Akt |
BD Biosciences |
Clone M89–61 |
| phospho-MTOR |
eBioscience |
Clone MRRBY |
| phospho-STAT3 |
BD Biosciences |
Clone 4 |
| CD16/CD32 (Fc Block) |
Tonbo |
Clone 2.4G2 |
| mCD8a |
BD Biosciences, BioLegend, Tonbo |
Clone H35–17.2 |
| mCD19 |
BD Biosciences, BioLegend, Tonbo |
Clone ID3 |
| mCD11b |
eBioscience |
Clone M1/70 |
| mCD3 (purified) |
BioLegend |
Clone 2C11 |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| CellTrace Violet |
Invitrogen |
Cat#C34571
|
| FoxP3 Staining Kit |
eBioscience |
Cat#00–5523-00 |
| GhostDye-Violet510 |
Tonbo Biosciences |
Cat#13–0870-T500 |
| RBC lysis buffer |
eBioscience |
Cat#00–4333-57 |
| Collagenase D |
Roche |
Cat#11088866001 |
| DNase I, type IV |
Sigma-Aldrich |
Cat#D5025 |
| Hyclone Fetal bovine serum |
Cytiva |
Cat#SH30071 |
| Tamoxifen |
MP Biomedical |
Cat#02156738-CF |
|
| Deposited data |
|
|
|
| RNA sequencing of Tim-3 Tg Treg and WT Treg |
Data obtained for this study |
GEO record GSE155825
|
| single-cell RNA sequencing of HNC tumors |
Cillo et al. (2020)
|
GEO record GSE139324
|
|
| Experimental models: Cell lines |
|
|
|
| MC38 tumor line |
Dario Vignali, Univ. of Pittsburgh |
RRID:CVCL_B288 |
| B16-F10 tumor line |
Dario Vignali, Univ. of Pittsburgh |
RRID:CVCL_0159 |
|
| Experimental models: Organisms/strains |
|
|
|
| Mouse: FoxP3eGFP-Cre-ERT2: Foxp3tm9(EGFP/cre/ERT2)Ayr
|
The Jackson Laboratory |
Cat#016961 |
| Mouse: Tim-3fl/fl: B6-Havcr2fl/fl
|
Developed with the Pitt Department of Immunolgy Transgenic and Gene Targeting Core for this study |
N/A |
| Mouse: FSF-Tim-3: B6-Rosa26flox-stop-flox-Flag-Tim-3
|
Developed for the investigators by GenOway |
Avery et al. (2018)
|
| Mouse: C57BL/6J |
The Jackson Laboratory |
Cat#000664 |
|
| Software and algorithms |
|
|
|
| FlowJo |
BD Biosciences |
version 10 |
| Prism |
GraphPad |
version 9 |
| FastQC |
Babraham Bioinformatics |
version 0.11.7 |
| Cutadapt |
https://cutadapt.readthedocs.io/en/stable/
|
version 1.18 |
| HISAT2 |
http://daehwankimlab.github.io/hisat2/main/
|
version 2.1.0 |
| SAMtools |
http://www.htslib.org/
|
version 1.9 |
| HTSeq |
https://htseq.readthedocs.io/en/master/
|
version 0.11.2 |
| Bioconductor edgeR |
https://bioconductor.org/packages/release/bioc/html/edgeR.html
|
version 3.24.1 |
| Enrichr |
https://maayanlab.cloud/Enrichr/
|
Kuleshov et al., 2016
|
| Scanpy |
https://github.com/theislab/scanpy
|
Wolf et al., 2018
|
