Journal: Cell reports

Article Title: Organoids capture tissue-specific innate lymphoid cell development in mice and humans.

doi: 10.1016/j.celrep.2022.111281

Figure Lengend Snippet: Figure 3. SIOs provide an essentially GF model of gut-specific ILCs (A) Representative flow plots of NKp46 expression in ILCP + SIO co-culture-derived ILCs or SI-LP-derived CD127+ ILCs, with the frequency of NKp46+ ILC3s (co- culture: Live, EpCAM, Lin, CD45+, RORgt+; primary tissue: Live, CD45+, Lin, CD127+, Klrg1, NK1.1+/, RORgt+) additionally quantified for ILCPs cultured without SIOs or with GF SIOs in (B) (N = 2–5 animals, pooled from two experiments). (C) Relative frequency of mature ILC subsets excluding immature or other cells, depicting group 1 (magenta; Live, EpCAM, CD45+, Lin, RORgt-, ST2, Klrg1, NK1.1+, NKp46+), group 2 (green; Live, EpCAM, CD45+, Lin, RORgt, NK1.1, ST2+, Klrg1+, Sca-1+), NKp46+ group 3 (lavender; Live, EpCAM, CD45+, Lin, ST2, Klrg1, RORgt+, NKp46+), and NKp46 group 3 ILCs (blue; Live, EpCAM, CD45+, Lin, ST2, Klrg1, RORgt+, NKp46) in live, unstimulated co-cultures derived from SPF-SIOs or GF-SIOs compared with primary SPF ileum (no Peyer’s patches). (D) Diagram of transwell culture strategy. (E) Relative frequency of group 1, 2, and 3 ILCs derived from PD-1+ ILCP + SIO +/ transwell insert (TW) separation (N = 3, two experiments).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human CRTh2 – PE Miltenyi Biotec Cat# 130-113-600 Human CRTh2– BV711 BioLegend Cat# 350124 Human CRTh2 – BV421 BioLegend Cat# 350112 Human CD161 APC, A700 BioLegend Cat# 302012 Human ST2 – APC R&D Sys Cat# FAB5231A Human ST2 – PE R&D Sys Cat# FAB5231P Human NKp44 – PE Cy7 BioLegend Cat# 325116 Human NKp44 – PerCP Cy5.5 BioLegend Cat# 325114 Human/Mouse Tbet – PE-Cy7 BioLegend Cat# 644824 Human RORgt – APC Thermofisher (eBioscience) Cat# 17-6988-82 Human RORgt – PE BDBiosciences Cat# 563081 Human GATA3 – APC Cy7 Santa Cruz Cat# sc-268 Human IL22 – PerCP Cy5.5 BioLegend Cat# 366709 Human IL17A – PE-Dazzle BioLegend Cat# 512335 Human IL17A – e450 BD Horizon/ bioscience Cat# 560610 Human IL17A – BV786 BD Horizon/ bioscience Cat# 563745 Human IFNg –APCe780 Invitrogen Cat# 47-7319-41 Human IL-5 – APC BioLegend Cat# 504305 Human IL-13 – FITC eBioscience Cat# 11-7139-41 Human IL-13 – bv711 BD Biosciences Cat# 564288 Human CD25 – PerCP-Cy 5.5 BD Biosciences Cat# 560503 Human Klrg1 – APC Thermofisher (eBioscience) Cat# 25-5893-80 Human CCR6 – APC BioLegend Cat# 353416 Human CCR6 – BV605 BioLegend Cat# 353419 Human NKp46 APC BioLegend Cat# 331918 FcR CD16/32 blocking, mouse BioCell Cat# BE0307 FcR blocking, human Miltenyi Biotec Cat# 130-059-901 Anti-rhIL33 (neutralising, ICC, goat polyclonal) R&D Cat# AF3625 Anti-rmIL33 (neutralising, ICC, goat polyclonal) R&D Cat# AF3626 E-Cadherin – anti-human (rat) Thermofisher (eBioscience) Cat# 51-3249-82 CDX2 – anti-human (rabbit) abcam Cat# Ab76541 EpCAM – anti-mouse (rabbit) abcam Cat# Ab71916 CD45 anti-human (mouse) BioLegend Cat# 304001 ZO-1 anti-mouse (rabbit) Abcam Cat# Ab96587 Dclk1 anti-mouse (rabbit) Abcam Cat# Ab31704 CD44 anti-mouse/human (rat) Thermofisher (eBioscience) Cat# 14-0551-82 Critical commercial assays CellTrace FarRed ThermoFischer Cat# C34564 Foxp3 / Transcription Factor Staining Buffer Set Invitrogen eBioscience Cat# 00-5523-00 Live Dead fixable blue/UV ThermoFischer Cat# L34961 UltraComp eBeads Invitrogen Cat# 01-2222-42 RNeasy Qiagen Cat# 74106 RevertAid First Strand cDNA Synthesis Kit ThermoFisher Cat# K1622 Fast SYBR green master mix Applied Biosystems Cat# 4385612 (Continued on next page) Cell Reports 40, 111281, August 30, 2022 e2

Techniques: Expressing, Co-Culture Assay, Derivative Assay, Cell Culture

Journal: Cell reports

Article Title: Organoids capture tissue-specific innate lymphoid cell development in mice and humans.

doi: 10.1016/j.celrep.2022.111281

Figure Lengend Snippet: Figure 7. Gut-matured ILC2 upregulates ST2 on transfer to HLO culture (A) Representative image of SD-HIOs and SD-HLOs showing E-cadherin+ (E-CAD) epithelium, CD45+ ILCs, and nuclei (Hoechst) after 14-day co-culture (scale bars: 50 mm). (B) Count of EpCAM, CD45+, LIN ILCs after 14-day co-culture with SD-HIOs or SD-HLOs, with corresponding count of EpCAM, CD45 mesenchyme.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human CRTh2 – PE Miltenyi Biotec Cat# 130-113-600 Human CRTh2– BV711 BioLegend Cat# 350124 Human CRTh2 – BV421 BioLegend Cat# 350112 Human CD161 APC, A700 BioLegend Cat# 302012 Human ST2 – APC R&D Sys Cat# FAB5231A Human ST2 – PE R&D Sys Cat# FAB5231P Human NKp44 – PE Cy7 BioLegend Cat# 325116 Human NKp44 – PerCP Cy5.5 BioLegend Cat# 325114 Human/Mouse Tbet – PE-Cy7 BioLegend Cat# 644824 Human RORgt – APC Thermofisher (eBioscience) Cat# 17-6988-82 Human RORgt – PE BDBiosciences Cat# 563081 Human GATA3 – APC Cy7 Santa Cruz Cat# sc-268 Human IL22 – PerCP Cy5.5 BioLegend Cat# 366709 Human IL17A – PE-Dazzle BioLegend Cat# 512335 Human IL17A – e450 BD Horizon/ bioscience Cat# 560610 Human IL17A – BV786 BD Horizon/ bioscience Cat# 563745 Human IFNg –APCe780 Invitrogen Cat# 47-7319-41 Human IL-5 – APC BioLegend Cat# 504305 Human IL-13 – FITC eBioscience Cat# 11-7139-41 Human IL-13 – bv711 BD Biosciences Cat# 564288 Human CD25 – PerCP-Cy 5.5 BD Biosciences Cat# 560503 Human Klrg1 – APC Thermofisher (eBioscience) Cat# 25-5893-80 Human CCR6 – APC BioLegend Cat# 353416 Human CCR6 – BV605 BioLegend Cat# 353419 Human NKp46 APC BioLegend Cat# 331918 FcR CD16/32 blocking, mouse BioCell Cat# BE0307 FcR blocking, human Miltenyi Biotec Cat# 130-059-901 Anti-rhIL33 (neutralising, ICC, goat polyclonal) R&D Cat# AF3625 Anti-rmIL33 (neutralising, ICC, goat polyclonal) R&D Cat# AF3626 E-Cadherin – anti-human (rat) Thermofisher (eBioscience) Cat# 51-3249-82 CDX2 – anti-human (rabbit) abcam Cat# Ab76541 EpCAM – anti-mouse (rabbit) abcam Cat# Ab71916 CD45 anti-human (mouse) BioLegend Cat# 304001 ZO-1 anti-mouse (rabbit) Abcam Cat# Ab96587 Dclk1 anti-mouse (rabbit) Abcam Cat# Ab31704 CD44 anti-mouse/human (rat) Thermofisher (eBioscience) Cat# 14-0551-82 Critical commercial assays CellTrace FarRed ThermoFischer Cat# C34564 Foxp3 / Transcription Factor Staining Buffer Set Invitrogen eBioscience Cat# 00-5523-00 Live Dead fixable blue/UV ThermoFischer Cat# L34961 UltraComp eBeads Invitrogen Cat# 01-2222-42 RNeasy Qiagen Cat# 74106 RevertAid First Strand cDNA Synthesis Kit ThermoFisher Cat# K1622 Fast SYBR green master mix Applied Biosystems Cat# 4385612 (Continued on next page) Cell Reports 40, 111281, August 30, 2022 e2

Techniques: Co-Culture Assay

Journal: The journal of applied laboratory medicine

Article Title: Plasma Protein Profiling by Proximity Extension Assay Technology Reveals Novel Biomarkers of Traumatic Brain Injury-A Pilot Study.

doi: 10.1093/jalm/jfab004

Figure Lengend Snippet: Fig. 1. Normalized protein expression (NPX) of plasma biomarkers in surviving [sTBI (S); n 5 6] and non- surviving sTBI patients [sTBI (NS); n 5 4] compared with matched healthy controls (CTR, n 5 10). Biomarkers shown are (A) ST2, (B) IL6, (C) TNNI3, (D) TNFR-2, (E) CHI3L1, and (F) EN-RAGE. Reference groups shown are ovarian cancer patients (OvCa, n 5 32) and dementia patients (mild cognitive impair- ment, MCI, n 5 18; Alzheimer disease, AD, n 5 12). Dotted lines represent group median, bars show interquartile range. Mann Whitney U test; *P < 0.05, **P < 0.01, ***P < 0.001, ns, not significant. For more discussion see text.

Article Snippet: All sTBI and matched control samples were analyzed in duplicate using the commercially available ELISA kits, DRT200 TNFR2 Quantikine kit and the DST200 ST2 Quantikine kit (R&D Systems), according to manufacturer’s instructions.

Techniques: Expressing, Clinical Proteomics, MANN-WHITNEY

Journal: The journal of applied laboratory medicine

Article Title: Plasma Protein Profiling by Proximity Extension Assay Technology Reveals Novel Biomarkers of Traumatic Brain Injury-A Pilot Study.

doi: 10.1093/jalm/jfab004

Figure Lengend Snippet: Fig. 3. Plasma concentration of ST2 and TNFR-2 in healthy controls (n 5 10) and sTBI patients (n 5 10), as measured by commercially available ELISAs. Mann Whitney U test; ****P < 0.0001. For more details see text.

Article Snippet: All sTBI and matched control samples were analyzed in duplicate using the commercially available ELISA kits, DRT200 TNFR2 Quantikine kit and the DST200 ST2 Quantikine kit (R&D Systems), according to manufacturer’s instructions.

Techniques: Clinical Proteomics, Concentration Assay, MANN-WHITNEY

Journal: The journal of applied laboratory medicine

Article Title: Plasma Protein Profiling by Proximity Extension Assay Technology Reveals Novel Biomarkers of Traumatic Brain Injury-A Pilot Study.

doi: 10.1093/jalm/jfab004

Figure Lengend Snippet: Fig. 4. Comparison between commercially available proximity extension assays (Olink Proteomics) and ELISAs. Plasma ST2 was measured in (A) healthy controls (n 5 10); Spearman’s correlation (rs) 5 0.8909, P 5 0.0011, and (B) sTBI patients (n 5 10); rs 5 0.9758, P < 0.0001. Plasma TNFR-2 was measured in (A) healthy controls (n 5 10); rs 5 0.9030, P 5 0.0008, and (B) sTBI patients (n 5 10); rs 5 0.8667, P 5 0.0022. Black line shows line of best fit.

Article Snippet: All sTBI and matched control samples were analyzed in duplicate using the commercially available ELISA kits, DRT200 TNFR2 Quantikine kit and the DST200 ST2 Quantikine kit (R&D Systems), according to manufacturer’s instructions.

Techniques: Comparison, Clinical Proteomics