Journal: Frontiers in Plant Science

Article Title: A Grapevine TTG2-Like WRKY Transcription Factor Is Involved in Regulating Vacuolar Transport and Flavonoid Biosynthesis

doi: 10.3389/fpls.2016.01979

Figure Lengend Snippet: Expression analyses in petunia petals by qPCR. (A) Expression analysis of F3 ′ H and N21 in the ph3 mutant and in VvWRKY26 expressing lines as confirmation of the microarray results. (B) Expression analysis of structural genes related to vacuolar acidification (PhPH5 and PhPH1) and to anthocyanin synthesis (PhCHS-A and PhDFR-A) in the untransformed R27 and ph3 lines and VvWRKY26 expressing plants. In all analyses the data correspond to the mean ± SE of three biological replicates (corresponding to lines 1, 2, and 5; Supplementary Figure ) relative to an ACTIN housekeeping control and normalized against the ph3 mutant value. Abbreviations correspond to: PhF3 ′ H, FLAVONOID-3 ′ -MONOOXYGENASE; PhN21, NODULIN MTN21-LIKE PROTEIN; PhPH5, H + P 3 A -ATPASE; PhPH1, P 3 B -ATPASE; PhCHS-A, CHALCONE SYNTHASE A; PhDFR-A, DIHYDROFLAVONOL 4-REDUCTASE A .

Article Snippet: For microarray analysis on Sultana leaves transiently over-expressing VvWRKY26 , the cDNA synthesis, labeling, hybridization and washing reactions were performed according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

Techniques: Expressing, Mutagenesis, Microarray

Journal: American Journal of Cancer Research

Article Title: Detection and application of circulating tumor cell and circulating tumor DNA in the non-small cell lung cancer

doi:

Figure Lengend Snippet: Compare the differences between circulating tumor cell (CTCs) and circulating tumor DNA (ctDNA)

Article Snippet: Other researches also confirmed these results [ 86 , 87 ] ( ). table ft1 table-wrap mode="anchored" t5 caption a7 Comparison CTCs ctDNA Definition Tumor cells are released into the blood from primary tumors and/or metastatic sites [ 9 ] High concentration of cell-free DNA in tumor patients [ 24 ] Common detection technology CellSearch method (Janssen Diagnostics Company, USA) [ 17 ]/FISHMAN-R/On-chip Sort [ 20 , 21 ] Conventional approach (karyotype analysis) Molecular cytogenetic methods (spectral karyotyping, CGH and FISH) Modern technologies (microarray-based CGH, SNP, NGS) [ 26 ] PCR-based methods (microfluidics digital PCR, ddPCR [ 30 , 31 ] Information type providing by analysis DNA, RNA and protein [ 7 , 9 ] DNA [ 7 , 9 ] As diagnostic biomarkers CTC counts contributes to the judgment of benign and malignant lung diseases [ 36 , 37 ] Prone to the diagnosis of molecular subtypes of lung cancer [ 40 - 45 ] As prognostic biomarkers Assess the change of patient’s condition by monitoring the proliferation and apoptosis changes of CTCs [ 51 ] CtDNA A can be used as an independent prognostic marker [ 13 , 56 , 58 ] The number of CTCs is significantly related to DFS and PFS [ 52 , 53 ] Different mutation status of the same subtype has a different prognosis [ 57 ] Roles of CTC and ctDNA in targeted therapy Baseline CTC counts can be used to predict and monitor the efficacy of targeted therapies [ 69 ] Monitor mutation status to guide the selection of targeted drugs [ 65 - 67 ] Open in a separate window Compare the differences between circulating tumor cell (CTCs) and circulating tumor DNA (ctDNA)

Techniques: Concentration Assay, Microarray, Next-Generation Sequencing, Digital PCR, Diagnostic Assay, Marker, Mutagenesis, Selection

Journal: Cell

Article Title: A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

doi: 10.1016/j.cell.2016.08.052

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-PD-1 (clone: RMP1-30) Biolegend Cat#: 109109 Anti-Tim3 (clone: 5D12) Generated in house N/A Rat anti-IL-2 (clone: JES6-5H4) Biolegend Cat#: 503807 Anti-TNF-α (clone: MP6-XT22), eBioscience Cat#: 117321 Anti-IFN-γ (clone: XMG-1.2) Biolegend Cat# 505829 Mouse anti-Granzyme B (clone: GB11) Biolegend Cat#: 515405 Rat anti-CD8 (clone: 53–6.7) Biolegend Cat# 100731 Chemicals, Peptides, and Recombinant Proteins Zinpyr-1 Santa Cruz Cat#: sc-213182 Fixable viability dye eFluor506 eBioscience Cat#: 65-0866 Gp100 Genscript Cat#: RP20344 Critical Commercial Assays High Sensitivity DNA Kit (Bioanalyzer) Agilent Cat#: 5067-4626 Qubit dsDNA, High Sensitivity 500rxn Thermo Fisher Scientific Cat#: {"type":"entrez-protein","attrs":{"text":"Q32854","term_id":"75280861","term_text":"Q32854"}} Q32854 Nextera XT Sample Preparation Kit Illumina Cat#: FC-131-1096 NextSeq 500 high output kit V2, 75 cycles Illumina Cat#: FC-404-2005 Deposited Data Data files for CD8+ populations, Microarray This paper need to get accession number Data files for bulk RNA sequencing This paper need to get accession number Data files for single-cell RNA sequencing This paper need to get accession number LCMV exhaustion signature ( Doering et al., 2012 ) {"type":"entrez-geo","attrs":{"text":"GSE41867","term_id":"41867"}} GSE41867 CD8 + Ly49 + Treg signature ( Kim et al., 2015 ) {"type":"entrez-geo","attrs":{"text":"GSE73015","term_id":"73015"}} GSE73015 Experimental Models: Cell Lines MC38-OVA Mark Smyth N/A CT26 ATCC Cat#: CRL-2638 B16-F10 ATCC Cat#: CRL-6475 Experimental Models: Organisms/Strains Balb/c Jackson Laboratory Cat#: 000651 C57BL/6 Jackson Laboratory Cat#: 000664 PMEL Jackson Laboratory Cat#: 005023 OTI Jackson Laboratory Cat#: 003831 MT −/− (backcrossed to C57BL/6 in house) Jackson Laboratory Cat#: 002211 Recombinant DNA SMARTER TSO (with LNA, 10 µM)) Exiqon 5’- AAGCAGTGGTATC AACGCAGAGTACr GrG+G-3’ PCR oligonucleotide primer (10 µM) IDT 5’- AAGCAGTGGTATC AACGCAGAGT-3 Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 µM) IDT 5- AAGCAGTGGTATC AACGCAGAGTACT (30)VN-3 Sequence-Based Reagents Gata3 CRISPR guide sequence Designed in house 5’ - GGTATCCTCCGAC CCACCACG Software and Algorithms GenePattern ( Reich et al., 2006 ) http://software.broadinstitute.org/cancer/software/genepattern/ COMBAT ( Johnson et al., 2007 ) http://www.bu.edu/jlab/wp-assets/ComBat/Download.html Bowtie ( Langmead et al., 2009 ) http://bowtie-bio.sourceforge.net/index.shtml RSEM ( Li and Dewey, 2011 ) http://deweylab.github.io/RSEM/ XL-mHG ( Wagner, 2015 ) https://github.com/flocompbio/xlmhg Other Open in a separate window KEY RESOURCES TABLE Distinct gene modules for T cell dysfunction and activation can be uncoupled.

Techniques: Generated, Recombinant, Sample Prep, Microarray, RNA Sequencing Assay, Sequencing, CRISPR, Software

Journal: Cell

Article Title: A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

doi: 10.1016/j.cell.2016.08.052

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-PD-1 (clone: RMP1-30) Biolegend Cat#: 109109 Anti-Tim3 (clone: 5D12) Generated in house N/A Rat anti-IL-2 (clone: JES6-5H4) Biolegend Cat#: 503807 Anti-TNF-α (clone: MP6-XT22), eBioscience Cat#: 117321 Anti-IFN-γ (clone: XMG-1.2) Biolegend Cat# 505829 Mouse anti-Granzyme B (clone: GB11) Biolegend Cat#: 515405 Rat anti-CD8 (clone: 53–6.7) Biolegend Cat# 100731 Chemicals, Peptides, and Recombinant Proteins Zinpyr-1 Santa Cruz Cat#: sc-213182 Fixable viability dye eFluor506 eBioscience Cat#: 65-0866 Gp100 Genscript Cat#: RP20344 Critical Commercial Assays High Sensitivity DNA Kit (Bioanalyzer) Agilent Cat#: 5067-4626 Qubit dsDNA, High Sensitivity 500rxn Thermo Fisher Scientific Cat#: {"type":"entrez-protein","attrs":{"text":"Q32854","term_id":"75280861","term_text":"Q32854"}} Q32854 Nextera XT Sample Preparation Kit Illumina Cat#: FC-131-1096 NextSeq 500 high output kit V2, 75 cycles Illumina Cat#: FC-404-2005 Deposited Data Data files for CD8+ populations, Microarray This paper need to get accession number Data files for bulk RNA sequencing This paper need to get accession number Data files for single-cell RNA sequencing This paper need to get accession number LCMV exhaustion signature ( Doering et al., 2012 ) {"type":"entrez-geo","attrs":{"text":"GSE41867","term_id":"41867"}} GSE41867 CD8 + Ly49 + Treg signature ( Kim et al., 2015 ) {"type":"entrez-geo","attrs":{"text":"GSE73015","term_id":"73015"}} GSE73015 Experimental Models: Cell Lines MC38-OVA Mark Smyth N/A CT26 ATCC Cat#: CRL-2638 B16-F10 ATCC Cat#: CRL-6475 Experimental Models: Organisms/Strains Balb/c Jackson Laboratory Cat#: 000651 C57BL/6 Jackson Laboratory Cat#: 000664 PMEL Jackson Laboratory Cat#: 005023 OTI Jackson Laboratory Cat#: 003831 MT −/− (backcrossed to C57BL/6 in house) Jackson Laboratory Cat#: 002211 Recombinant DNA SMARTER TSO (with LNA, 10 μM)) Exiqon 5’- AAGCAGTGGTATC AACGCAGAGTACr GrG+G-3’ PCR oligonucleotide primer (10 μM) IDT 5’- AAGCAGTGGTATC AACGCAGAGT-3 Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 μM) IDT 5- AAGCAGTGGTATC AACGCAGAGTACT (30)VN-3 Sequence-Based Reagents Gata3 CRISPR guide sequence Designed in house 5’ - GGTATCCTCCGAC CCACCACG Software and Algorithms GenePattern ( Reich et al., 2006 ) http://software.broadinstitute.org/cancer/software/genepattern/ COMBAT ( Johnson et al., 2007 ) http://www.bu.edu/jlab/wp-assets/ComBat/Download.html Bowtie ( Langmead et al., 2009 ) http://bowtie-bio.sourceforge.net/index.shtml RSEM ( Li and Dewey, 2011 ) http://deweylab.github.io/RSEM/ XL-mHG ( Wagner, 2015 ) https://github.com/flocompbio/xlmhg Other Open in a separate window KEY RESOURCES TABLE Distinct gene modules for T cell dysfunction and activation can be uncoupled.

Techniques: Generated, Recombinant, Sample Prep, Microarray, RNA Sequencing, Reverse Transcription, Sequencing, CRISPR, Software

Journal: Cell

Article Title: A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

doi: 10.1016/j.cell.2016.08.052

Figure Lengend Snippet: (A–B). Mice deficient in both MT1 and MT2 (MT−/−) and wild type (WT) littermate controls were implanted subcutaneously with B16F10 melanoma. A) Mean tumor growth. Statistical analysis was performed using linear regression ***p-value < 0.001. B) Tumor draining Lymph node (dLN, upper panel) and tumor-infiltrating lymphocytes (TIL, lower panel) were isolated from WT and MT−/− mice 15 days post tumor inoculation and stimulated with tumor antigen gp100. On day 3, tumor antigen-specific proliferation was measured by 3H incorporation. C) Naïve OT-1 cells were sorted, activated, and infected with empty retrovirus (control OT1) or MT1 retrovirus (MT OT1) prior to transfer (1 ×106 cells/mouse) into WT mice that were subsequently implanted with MC38-OVA tumor the next day. Mean tumor growth is shown. Statistical analysis was performed using linear regression **p-value < 0.01. D-E) MT−/− CD8+ TILs have increased functionality as compared to WT CD8+ TILs. TILs were isolated and stimulated with PMA/ionomyicin in the presence of brefeldin A for 4 hours prior to extracellular and intracellular staining and analysis by flow cytometry. *p-value < 0.05. F) Tim-3 and PD-1 expression in WT and MT−/− TILs. The DN, SP, and DP subpopulations are present in both the WT and MT−/− TILs. See also Suppl Fig 2.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-PD-1 (clone: RMP1-30) Biolegend Cat#: 109109 Anti-Tim3 (clone: 5D12) Generated in house N/A Rat anti-IL-2 (clone: JES6-5H4) Biolegend Cat#: 503807 Anti-TNF-α (clone: MP6-XT22), eBioscience Cat#: 117321 Anti-IFN-γ (clone: XMG-1.2) Biolegend Cat# 505829 Mouse anti-Granzyme B (clone: GB11) Biolegend Cat#: 515405 Rat anti-CD8 (clone: 53–6.7) Biolegend Cat# 100731 Chemicals, Peptides, and Recombinant Proteins Zinpyr-1 Santa Cruz Cat#: sc-213182 Fixable viability dye eFluor506 eBioscience Cat#: 65-0866 Gp100 Genscript Cat#: RP20344 Critical Commercial Assays High Sensitivity DNA Kit (Bioanalyzer) Agilent Cat#: 5067-4626 Qubit dsDNA, High Sensitivity 500rxn Thermo Fisher Scientific Cat#: {"type":"entrez-protein","attrs":{"text":"Q32854","term_id":"75280861","term_text":"Q32854"}} Q32854 Nextera XT Sample Preparation Kit Illumina Cat#: FC-131-1096 NextSeq 500 high output kit V2, 75 cycles Illumina Cat#: FC-404-2005 Deposited Data Data files for CD8+ populations, Microarray This paper need to get accession number Data files for bulk RNA sequencing This paper need to get accession number Data files for single-cell RNA sequencing This paper need to get accession number LCMV exhaustion signature ( Doering et al., 2012 ) {"type":"entrez-geo","attrs":{"text":"GSE41867","term_id":"41867"}} GSE41867 CD8 + Ly49 + Treg signature ( Kim et al., 2015 ) {"type":"entrez-geo","attrs":{"text":"GSE73015","term_id":"73015"}} GSE73015 Experimental Models: Cell Lines MC38-OVA Mark Smyth N/A CT26 ATCC Cat#: CRL-2638 B16-F10 ATCC Cat#: CRL-6475 Experimental Models: Organisms/Strains Balb/c Jackson Laboratory Cat#: 000651 C57BL/6 Jackson Laboratory Cat#: 000664 PMEL Jackson Laboratory Cat#: 005023 OTI Jackson Laboratory Cat#: 003831 MT −/− (backcrossed to C57BL/6 in house) Jackson Laboratory Cat#: 002211 Recombinant DNA SMARTER TSO (with LNA, 10 μM)) Exiqon 5’- AAGCAGTGGTATC AACGCAGAGTACr GrG+G-3’ PCR oligonucleotide primer (10 μM) IDT 5’- AAGCAGTGGTATC AACGCAGAGT-3 Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 μM) IDT 5- AAGCAGTGGTATC AACGCAGAGTACT (30)VN-3 Sequence-Based Reagents Gata3 CRISPR guide sequence Designed in house 5’ - GGTATCCTCCGAC CCACCACG Software and Algorithms GenePattern ( Reich et al., 2006 ) http://software.broadinstitute.org/cancer/software/genepattern/ COMBAT ( Johnson et al., 2007 ) http://www.bu.edu/jlab/wp-assets/ComBat/Download.html Bowtie ( Langmead et al., 2009 ) http://bowtie-bio.sourceforge.net/index.shtml RSEM ( Li and Dewey, 2011 ) http://deweylab.github.io/RSEM/ XL-mHG ( Wagner, 2015 ) https://github.com/flocompbio/xlmhg Other Open in a separate window KEY RESOURCES TABLE Distinct gene modules for T cell dysfunction and activation can be uncoupled.

Techniques: Isolation, Infection, Control, Staining, Flow Cytometry, Expressing

Journal: Cell

Article Title: A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

doi: 10.1016/j.cell.2016.08.052

Figure Lengend Snippet: A) Gata3, a zinc-binding TF, ranks first in the dysfunction module. B and C) WT mice were implanted subcutaneously with B16F10 melanoma cells. TILs were isolated on day 15 and analyzed for Gata3 expression and T cell function. B) Representative flow cytometry data showing Gata3 expression gated on CD8+ TILs. C) Cytokine expression of Gata3+ and Gata3CD8+ TILs. Statistical analysis was performed using paired student t test. *p-value < 0.05, *** p-value < 0.001. D) Targeted deletion of Gata3 using CRISPR/Cas9 genome editing. Naïve CD8+ T cells were sorted from pmel transgenic mice, infected with control or Gata3 lentivirus and activated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of IL-2 (Methods and Resources). Representative qPCR results showing Gata3 mRNA level in control versus Gata3 lentivirus targeted CD8+ T cells. E) 1 × 106 CRISPR/Cas9-targeted cells were transferred to WT mice (n=5/group) bearing B16F10 melanoma tumors (day 5 post tumor grafting). Mean tumor growth is shown. Data are representative of 3 independent experiments. Statistical analysis was performed using linear regression. **p-value < 0.01. F and G) TILs were isolated on day 21 after tumor cell injection and analyzed for Tim-3 and PD-1 expression (F) and cytokine production (G) by flow cytometry.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-PD-1 (clone: RMP1-30) Biolegend Cat#: 109109 Anti-Tim3 (clone: 5D12) Generated in house N/A Rat anti-IL-2 (clone: JES6-5H4) Biolegend Cat#: 503807 Anti-TNF-α (clone: MP6-XT22), eBioscience Cat#: 117321 Anti-IFN-γ (clone: XMG-1.2) Biolegend Cat# 505829 Mouse anti-Granzyme B (clone: GB11) Biolegend Cat#: 515405 Rat anti-CD8 (clone: 53–6.7) Biolegend Cat# 100731 Chemicals, Peptides, and Recombinant Proteins Zinpyr-1 Santa Cruz Cat#: sc-213182 Fixable viability dye eFluor506 eBioscience Cat#: 65-0866 Gp100 Genscript Cat#: RP20344 Critical Commercial Assays High Sensitivity DNA Kit (Bioanalyzer) Agilent Cat#: 5067-4626 Qubit dsDNA, High Sensitivity 500rxn Thermo Fisher Scientific Cat#: {"type":"entrez-protein","attrs":{"text":"Q32854","term_id":"75280861","term_text":"Q32854"}} Q32854 Nextera XT Sample Preparation Kit Illumina Cat#: FC-131-1096 NextSeq 500 high output kit V2, 75 cycles Illumina Cat#: FC-404-2005 Deposited Data Data files for CD8+ populations, Microarray This paper need to get accession number Data files for bulk RNA sequencing This paper need to get accession number Data files for single-cell RNA sequencing This paper need to get accession number LCMV exhaustion signature ( Doering et al., 2012 ) {"type":"entrez-geo","attrs":{"text":"GSE41867","term_id":"41867"}} GSE41867 CD8 + Ly49 + Treg signature ( Kim et al., 2015 ) {"type":"entrez-geo","attrs":{"text":"GSE73015","term_id":"73015"}} GSE73015 Experimental Models: Cell Lines MC38-OVA Mark Smyth N/A CT26 ATCC Cat#: CRL-2638 B16-F10 ATCC Cat#: CRL-6475 Experimental Models: Organisms/Strains Balb/c Jackson Laboratory Cat#: 000651 C57BL/6 Jackson Laboratory Cat#: 000664 PMEL Jackson Laboratory Cat#: 005023 OTI Jackson Laboratory Cat#: 003831 MT −/− (backcrossed to C57BL/6 in house) Jackson Laboratory Cat#: 002211 Recombinant DNA SMARTER TSO (with LNA, 10 μM)) Exiqon 5’- AAGCAGTGGTATC AACGCAGAGTACr GrG+G-3’ PCR oligonucleotide primer (10 μM) IDT 5’- AAGCAGTGGTATC AACGCAGAGT-3 Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 μM) IDT 5- AAGCAGTGGTATC AACGCAGAGTACT (30)VN-3 Sequence-Based Reagents Gata3 CRISPR guide sequence Designed in house 5’ - GGTATCCTCCGAC CCACCACG Software and Algorithms GenePattern ( Reich et al., 2006 ) http://software.broadinstitute.org/cancer/software/genepattern/ COMBAT ( Johnson et al., 2007 ) http://www.bu.edu/jlab/wp-assets/ComBat/Download.html Bowtie ( Langmead et al., 2009 ) http://bowtie-bio.sourceforge.net/index.shtml RSEM ( Li and Dewey, 2011 ) http://deweylab.github.io/RSEM/ XL-mHG ( Wagner, 2015 ) https://github.com/flocompbio/xlmhg Other Open in a separate window KEY RESOURCES TABLE Distinct gene modules for T cell dysfunction and activation can be uncoupled.

Techniques: Binding Assay, Isolation, Expressing, Cell Function Assay, Flow Cytometry, CRISPR, Transgenic Assay, Infection, Control, Injection

Journal: Cell

Article Title: A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

doi: 10.1016/j.cell.2016.08.052

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-PD-1 (clone: RMP1-30) Biolegend Cat#: 109109 Anti-Tim3 (clone: 5D12) Generated in house N/A Rat anti-IL-2 (clone: JES6-5H4) Biolegend Cat#: 503807 Anti-TNF-α (clone: MP6-XT22), eBioscience Cat#: 117321 Anti-IFN-γ (clone: XMG-1.2) Biolegend Cat# 505829 Mouse anti-Granzyme B (clone: GB11) Biolegend Cat#: 515405 Rat anti-CD8 (clone: 53–6.7) Biolegend Cat# 100731 Chemicals, Peptides, and Recombinant Proteins Zinpyr-1 Santa Cruz Cat#: sc-213182 Fixable viability dye eFluor506 eBioscience Cat#: 65-0866 Gp100 Genscript Cat#: RP20344 Critical Commercial Assays High Sensitivity DNA Kit (Bioanalyzer) Agilent Cat#: 5067-4626 Qubit dsDNA, High Sensitivity 500rxn Thermo Fisher Scientific Cat#: {"type":"entrez-protein","attrs":{"text":"Q32854","term_id":"75280861","term_text":"Q32854"}} Q32854 Nextera XT Sample Preparation Kit Illumina Cat#: FC-131-1096 NextSeq 500 high output kit V2, 75 cycles Illumina Cat#: FC-404-2005 Deposited Data Data files for CD8+ populations, Microarray This paper need to get accession number Data files for bulk RNA sequencing This paper need to get accession number Data files for single-cell RNA sequencing This paper need to get accession number LCMV exhaustion signature ( Doering et al., 2012 ) {"type":"entrez-geo","attrs":{"text":"GSE41867","term_id":"41867"}} GSE41867 CD8 + Ly49 + Treg signature ( Kim et al., 2015 ) {"type":"entrez-geo","attrs":{"text":"GSE73015","term_id":"73015"}} GSE73015 Experimental Models: Cell Lines MC38-OVA Mark Smyth N/A CT26 ATCC Cat#: CRL-2638 B16-F10 ATCC Cat#: CRL-6475 Experimental Models: Organisms/Strains Balb/c Jackson Laboratory Cat#: 000651 C57BL/6 Jackson Laboratory Cat#: 000664 PMEL Jackson Laboratory Cat#: 005023 OTI Jackson Laboratory Cat#: 003831 MT −/− (backcrossed to C57BL/6 in house) Jackson Laboratory Cat#: 002211 Recombinant DNA SMARTER TSO (with LNA, 10 μM)) Exiqon 5’- AAGCAGTGGTATC AACGCAGAGTACr GrG+G-3’ PCR oligonucleotide primer (10 μM) IDT 5’- AAGCAGTGGTATC AACGCAGAGT-3 Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 μM) IDT 5- AAGCAGTGGTATC AACGCAGAGTACT (30)VN-3 Sequence-Based Reagents Gata3 CRISPR guide sequence Designed in house 5’ - GGTATCCTCCGAC CCACCACG Software and Algorithms GenePattern ( Reich et al., 2006 ) http://software.broadinstitute.org/cancer/software/genepattern/ COMBAT ( Johnson et al., 2007 ) http://www.bu.edu/jlab/wp-assets/ComBat/Download.html Bowtie ( Langmead et al., 2009 ) http://bowtie-bio.sourceforge.net/index.shtml RSEM ( Li and Dewey, 2011 ) http://deweylab.github.io/RSEM/ XL-mHG ( Wagner, 2015 ) https://github.com/flocompbio/xlmhg Other Open in a separate window KEY RESOURCES TABLE Distinct gene modules for T cell dysfunction and activation can be uncoupled.

Techniques: Generated, Recombinant, Sample Prep, Microarray, RNA Sequencing, Reverse Transcription, Sequencing, CRISPR, Software

Journal: Cell

Article Title: A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

doi: 10.1016/j.cell.2016.08.052

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-PD-1 (clone: RMP1-30) Biolegend Cat#: 109109 Anti-Tim3 (clone: 5D12) Generated in house N/A Rat anti-IL-2 (clone: JES6-5H4) Biolegend Cat#: 503807 Anti-TNF-α (clone: MP6-XT22), eBioscience Cat#: 117321 Anti-IFN-γ (clone: XMG-1.2) Biolegend Cat# 505829 Mouse anti-Granzyme B (clone: GB11) Biolegend Cat#: 515405 Rat anti-CD8 (clone: 53–6.7) Biolegend Cat# 100731 Chemicals, Peptides, and Recombinant Proteins Zinpyr-1 Santa Cruz Cat#: sc-213182 Fixable viability dye eFluor506 eBioscience Cat#: 65-0866 Gp100 Genscript Cat#: RP20344 Critical Commercial Assays High Sensitivity DNA Kit (Bioanalyzer) Agilent Cat#: 5067-4626 Qubit dsDNA, High Sensitivity 500rxn Thermo Fisher Scientific Cat#: {"type":"entrez-protein","attrs":{"text":"Q32854","term_id":"75280861","term_text":"Q32854"}} Q32854 Nextera XT Sample Preparation Kit Illumina Cat#: FC-131-1096 NextSeq 500 high output kit V2, 75 cycles Illumina Cat#: FC-404-2005 Deposited Data Data files for CD8+ populations, Microarray This paper need to get accession number Data files for bulk RNA sequencing This paper need to get accession number Data files for single-cell RNA sequencing This paper need to get accession number LCMV exhaustion signature ( Doering et al., 2012 ) {"type":"entrez-geo","attrs":{"text":"GSE41867","term_id":"41867"}} GSE41867 CD8 + Ly49 + Treg signature ( Kim et al., 2015 ) {"type":"entrez-geo","attrs":{"text":"GSE73015","term_id":"73015"}} GSE73015 Experimental Models: Cell Lines MC38-OVA Mark Smyth N/A CT26 ATCC Cat#: CRL-2638 B16-F10 ATCC Cat#: CRL-6475 Experimental Models: Organisms/Strains Balb/c Jackson Laboratory Cat#: 000651 C57BL/6 Jackson Laboratory Cat#: 000664 PMEL Jackson Laboratory Cat#: 005023 OTI Jackson Laboratory Cat#: 003831 MT −/− (backcrossed to C57BL/6 in house) Jackson Laboratory Cat#: 002211 Recombinant DNA SMARTER TSO (with LNA, 10 μM)) Exiqon 5’- AAGCAGTGGTATC AACGCAGAGTACr GrG+G-3’ PCR oligonucleotide primer (10 μM) IDT 5’- AAGCAGTGGTATC AACGCAGAGT-3 Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 μM) IDT 5- AAGCAGTGGTATC AACGCAGAGTACT (30)VN-3 Sequence-Based Reagents Gata3 CRISPR guide sequence Designed in house 5’ - GGTATCCTCCGAC CCACCACG Software and Algorithms GenePattern ( Reich et al., 2006 ) http://software.broadinstitute.org/cancer/software/genepattern/ COMBAT ( Johnson et al., 2007 ) http://www.bu.edu/jlab/wp-assets/ComBat/Download.html Bowtie ( Langmead et al., 2009 ) http://bowtie-bio.sourceforge.net/index.shtml RSEM ( Li and Dewey, 2011 ) http://deweylab.github.io/RSEM/ XL-mHG ( Wagner, 2015 ) https://github.com/flocompbio/xlmhg Other Open in a separate window KEY RESOURCES TABLE Distinct gene modules for T cell dysfunction and activation can be uncoupled.

Techniques: Generated, Recombinant, Sample Prep, Microarray, RNA Sequencing, Reverse Transcription, Sequencing, CRISPR, Software

Journal: Cell

Article Title: A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

doi: 10.1016/j.cell.2016.08.052

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-PD-1 (clone: RMP1-30) Biolegend Cat#: 109109 Anti-Tim3 (clone: 5D12) Generated in house N/A Rat anti-IL-2 (clone: JES6-5H4) Biolegend Cat#: 503807 Anti-TNF-α (clone: MP6-XT22), eBioscience Cat#: 117321 Anti-IFN-γ (clone: XMG-1.2) Biolegend Cat# 505829 Mouse anti-Granzyme B (clone: GB11) Biolegend Cat#: 515405 Rat anti-CD8 (clone: 53–6.7) Biolegend Cat# 100731 Chemicals, Peptides, and Recombinant Proteins Zinpyr-1 Santa Cruz Cat#: sc-213182 Fixable viability dye eFluor506 eBioscience Cat#: 65-0866 Gp100 Genscript Cat#: RP20344 Critical Commercial Assays High Sensitivity DNA Kit (Bioanalyzer) Agilent Cat#: 5067-4626 Qubit dsDNA, High Sensitivity 500rxn Thermo Fisher Scientific Cat#: {"type":"entrez-protein","attrs":{"text":"Q32854","term_id":"75280861","term_text":"Q32854"}} Q32854 Nextera XT Sample Preparation Kit Illumina Cat#: FC-131-1096 NextSeq 500 high output kit V2, 75 cycles Illumina Cat#: FC-404-2005 Deposited Data Data files for CD8+ populations, Microarray This paper need to get accession number Data files for bulk RNA sequencing This paper need to get accession number Data files for single-cell RNA sequencing This paper need to get accession number LCMV exhaustion signature ( Doering et al., 2012 ) {"type":"entrez-geo","attrs":{"text":"GSE41867","term_id":"41867"}} GSE41867 CD8 + Ly49 + Treg signature ( Kim et al., 2015 ) {"type":"entrez-geo","attrs":{"text":"GSE73015","term_id":"73015"}} GSE73015 Experimental Models: Cell Lines MC38-OVA Mark Smyth N/A CT26 ATCC Cat#: CRL-2638 B16-F10 ATCC Cat#: CRL-6475 Experimental Models: Organisms/Strains Balb/c Jackson Laboratory Cat#: 000651 C57BL/6 Jackson Laboratory Cat#: 000664 PMEL Jackson Laboratory Cat#: 005023 OTI Jackson Laboratory Cat#: 003831 MT −/− (backcrossed to C57BL/6 in house) Jackson Laboratory Cat#: 002211 Recombinant DNA SMARTER TSO (with LNA, 10 µM)) Exiqon 5’- AAGCAGTGGTATC AACGCAGAGTACr GrG+G-3’ PCR oligonucleotide primer (10 µM) IDT 5’- AAGCAGTGGTATC AACGCAGAGT-3 Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 µM) IDT 5- AAGCAGTGGTATC AACGCAGAGTACT (30)VN-3 Sequence-Based Reagents Gata3 CRISPR guide sequence Designed in house 5’ - GGTATCCTCCGAC CCACCACG Software and Algorithms GenePattern ( Reich et al., 2006 ) http://software.broadinstitute.org/cancer/software/genepattern/ COMBAT ( Johnson et al., 2007 ) http://www.bu.edu/jlab/wp-assets/ComBat/Download.html Bowtie ( Langmead et al., 2009 ) http://bowtie-bio.sourceforge.net/index.shtml RSEM ( Li and Dewey, 2011 ) http://deweylab.github.io/RSEM/ XL-mHG ( Wagner, 2015 ) https://github.com/flocompbio/xlmhg Other Open in a separate window KEY RESOURCES TABLE Distinct gene modules for T cell dysfunction and activation can be uncoupled.

Techniques: Generated, Recombinant, Sample Prep, Microarray, RNA Sequencing Assay, Sequencing, CRISPR, Software

Journal: Cell

Article Title: A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

doi: 10.1016/j.cell.2016.08.052

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-PD-1 (clone: RMP1-30) Biolegend Cat#: 109109 Anti-Tim3 (clone: 5D12) Generated in house N/A Rat anti-IL-2 (clone: JES6-5H4) Biolegend Cat#: 503807 Anti-TNF-α (clone: MP6-XT22), eBioscience Cat#: 117321 Anti-IFN-γ (clone: XMG-1.2) Biolegend Cat# 505829 Mouse anti-Granzyme B (clone: GB11) Biolegend Cat#: 515405 Rat anti-CD8 (clone: 53–6.7) Biolegend Cat# 100731 Chemicals, Peptides, and Recombinant Proteins Zinpyr-1 Santa Cruz Cat#: sc-213182 Fixable viability dye eFluor506 eBioscience Cat#: 65-0866 Gp100 Genscript Cat#: RP20344 Critical Commercial Assays High Sensitivity DNA Kit (Bioanalyzer) Agilent Cat#: 5067-4626 Qubit dsDNA, High Sensitivity 500rxn Thermo Fisher Scientific Cat#: {"type":"entrez-protein","attrs":{"text":"Q32854","term_id":"75280861","term_text":"Q32854"}} Q32854 Nextera XT Sample Preparation Kit Illumina Cat#: FC-131-1096 NextSeq 500 high output kit V2, 75 cycles Illumina Cat#: FC-404-2005 Deposited Data Data files for CD8+ populations, Microarray This paper need to get accession number Data files for bulk RNA sequencing This paper need to get accession number Data files for single-cell RNA sequencing This paper need to get accession number LCMV exhaustion signature ( Doering et al., 2012 ) {"type":"entrez-geo","attrs":{"text":"GSE41867","term_id":"41867"}} GSE41867 CD8 + Ly49 + Treg signature ( Kim et al., 2015 ) {"type":"entrez-geo","attrs":{"text":"GSE73015","term_id":"73015"}} GSE73015 Experimental Models: Cell Lines MC38-OVA Mark Smyth N/A CT26 ATCC Cat#: CRL-2638 B16-F10 ATCC Cat#: CRL-6475 Experimental Models: Organisms/Strains Balb/c Jackson Laboratory Cat#: 000651 C57BL/6 Jackson Laboratory Cat#: 000664 PMEL Jackson Laboratory Cat#: 005023 OTI Jackson Laboratory Cat#: 003831 MT −/− (backcrossed to C57BL/6 in house) Jackson Laboratory Cat#: 002211 Recombinant DNA SMARTER TSO (with LNA, 10 µM)) Exiqon 5’- AAGCAGTGGTATC AACGCAGAGTACr GrG+G-3’ PCR oligonucleotide primer (10 µM) IDT 5’- AAGCAGTGGTATC AACGCAGAGT-3 Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 µM) IDT 5- AAGCAGTGGTATC AACGCAGAGTACT (30)VN-3 Sequence-Based Reagents Gata3 CRISPR guide sequence Designed in house 5’ - GGTATCCTCCGAC CCACCACG Software and Algorithms GenePattern ( Reich et al., 2006 ) http://software.broadinstitute.org/cancer/software/genepattern/ COMBAT ( Johnson et al., 2007 ) http://www.bu.edu/jlab/wp-assets/ComBat/Download.html Bowtie ( Langmead et al., 2009 ) http://bowtie-bio.sourceforge.net/index.shtml RSEM ( Li and Dewey, 2011 ) http://deweylab.github.io/RSEM/ XL-mHG ( Wagner, 2015 ) https://github.com/flocompbio/xlmhg Other Open in a separate window KEY RESOURCES TABLE Distinct gene modules for T cell dysfunction and activation can be uncoupled.

Techniques: Generated, Recombinant, Sample Prep, Microarray, RNA Sequencing Assay, Sequencing, CRISPR, Software