Staining:Article Title: The transcription factor Xrp1 orchestrates both reduced translation and cell competition upon defective ribosome assembly or function
Article Snippet: .. We used the following antibodies for staining: rabbit anti-phospho-RpS6 at 1:200 (1:200) , rabbit anti-p62 , rabbit anti-phospho-eIF2α at 1:100 (Thermofisher, 44–728 G, and Cell Signaling Technologies), rabbit anti-Xrp1 at 1:200 , mouse anti-b-Galactosidase (J1e7, DSHB), rabbit anti-GFP, rabbit anti-active-Dcp1 (Cell Signaling Techonology Cat#9578, 1:100), Y10b(1:100)(Thermofisher, MA1-13017), RpL9(1:100)(Abcam, ab50384),rabbit-anti-Rack1 (1:100) (Cell Signalling, D59D5), rabbit anti-hRpL10Ab (1:100) (Sigma, Cat# SAB1101199). .. Secondary Antibodies were Cy2- and Cy5- conjugates (Jackson Immunoresearch) or Alexa Fluor conjugates (Thermofisher).
Virus:
Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant Rabbit monoclonal anti-OGT HUABIO Cat# ET7107-17; RRID: AB_3070732 Mouse monoclonal anti- O-Linked N-Acetylglucosamine Abcam Cat# ab2739; RRID: AB_303264 Rabbit Polyclonal anti-beta Actin Servicebio Cat# GB11001; RRID: AB_2801259 Anti human Pancytokeratin Abcam Cat# ab234297; RRID:AB_ 2895302 Anti human CD4 Abcam Cat# ab133616; RRID: AB_2750883 Anti human CD8 Thermo Fisher Scientific Cat# MA1-80231; RRID: AB_929437 Anti human CD20 Cell Signaling Technology Cat# 48750S; RRID:AB_3107071 Anti human FOXP3 Cell Signaling Technology Cat# 98377; RRID: 2747370 Anti human CD68 Abcam Cat# ab280860; RRID: AB_2801637 Anti human CD163 Abcam Cat# ab182422; RRID: 2753196 Anti human CD86 Abcam Cat# ab220188; RRID: 3676334 Cyclin D1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1601-31; RRID: AB_3069614 Laminin beta 1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1703-14; RRID: AB_3070371 IL-18 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# HA721536; RRID: AB_3072652 AKT1/2/3 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1609-51; RRID: AB_2940862 Phospho-AKT (S473) Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1607-73; RRID: AB_2940863 PI 3 Kinase p85 alpha Recombinant Mouse Monoclonal Antibody HUABIO Cat# HA601206; RRID: AB_3071925 Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody Cell Signaling Technology Cat# 4228; RRID: 659940 Bacterial and virus strains Lentivirus: shRNA targeting OGT GenePharma Cat# D01001 Lentivirus: control shRNA GenePharma Cat# D03001 Lentivirus: OGT overexpression Generalbiol Cat# V1342936 Lentivirus: blank Generalbiol Cat# V1342935 Biological samples ESCC patient samples This paper N/A Chemicals, peptides, and recombinant proteins OSMI-1 Targetmol Cat# T16409 LY294002 Cayman Cat# 70920 D-Luciferin (potassium salt) Cayman chemical Cat# 14681 Puromycin Cayman chemical Cat# 13884 Critical commercial assays GP-transfect-Mate GenePharma Cat# G04008 Opal 7-Color Kit Akoya Biosciences N/A Superbrilliant® 6 min 1st Strand cDNA Synthesis Kit Zhongshi Gene Technology Cat# ZS-M14003 Superbrilliant® 2×ZAPA3G SYBR Green qPCR Mix Zhongshi Gene Technology Cat# ZS-M13002 Cell Counting Kit-8 MedChemExpress Cat# HY-K0301 (Continued on next page) e1 Cell Reports Medicine 7, 102650, March 17, 2026 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER PE Annexin V Apoptosis Detection Kit I BD Pharmingen Cat# 559763 PI/RNase Staining Buffer BD Pharmingen Cat# 554656 Deposited data Raw sequencing data This paper Genome Sequence Archive for Human (https:// cncb.ac.cn): HRA008846 TCGA datasets https://portal.gdc.cancer.gov N/A Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression Lin et al. 14 https://doi.org/10.1038/s41392-023-01710-2 Experimental models: Cell lines KYSE150 human ESCC cell line Haixing Biosciences TCH-C236 KYSE410 human ESCC cell line Haixing Biosciences TCH-C458 KYSE450 human ESCC cell line Servicebio STCC11902P KYSE30 human ESCC cell line Servicebio STCC11903P Experimental models: Organisms/strains Mouse: BALB/c-nu HFK Bioscience RRID:13001A Mouse: NOD SCID HFK Bioscience RRID:13002A Oligonucleotides Primers for RT-qPCR This paper N/A Recombinant DNA Plasmids and RNA interference sequences This paper N/A Software and algorithms GraphPad Prism 9 Graphpad software https://www.graphpad.com ImageJ https://imagej.net/ij/ R (v4.0.0) https://www.rproject.org GEPIA2 Zhang Lab 61 https://gepia2.cancer-pku.cn/ Seurat (v5.3.0) Hao et al. 62 https://satijalab.org/seurat/ edgeR (v4.6.2) Smyth et al. 63 https://bioconductor.org/packages/release/bioc/ html/edgeR.html clusterProfiler (V4.8.3) Yu et al. 64 N/A GeoMx NGS pipeline nanostring https://nanostring.com GeoMx DSP system nanostring https://nanostring.com ComplexHeatmap (v2.24.0) Gu et al. 65 https://bioconductor.org/packages/release/bioc/ html/ComplexHeatmap.html ggplot2 (v3.5.2) Pedersen et al. 66 https://tidyverse.r-universe.dev/ggplot2 Cibersort (v0.1.0) Alizadeh et al. 67 https://doi.org/10.1007/978-1-4939-7493-1_12 SpatialDecon (v1.18.0) Dandher et al. 68 https://doi.org/10.18129/B9.bioc.SpatialDecon ConsensusTME (v0.0.1) Miller et al. 69 https://doi.org/10.1158/0008-5472.CAN-18-3560 SCORPIUS (v1.0.9) Cannoodt et al. 70 https://github.com/rcannood/SCORPIUS CellChat (v1.5.0) Jin et al. 71 https://github.com/sqjin/CellChat STRING STRING Consortium 72 https://cn.string-db.org corrplot (v0.95) Wei et al. 73 https://github.com/taiyun/corrplot survival (v3.8-3) Therneau et al. 74 https://cran.r-project.org/web/packages/survival/ index.html survminer (v0.5.0) Kassambara et al. 75 https://cran.r-project.org/web/packages/ survminer/index.html Form (v2.4.4) Akoya Biosciences https://www.pubcompare.ai/product/ zzPiCZIBPBHhf-iFwRy1/ Cell Reports Medicine 7, 102650, March 17, 2026 e2 OPEN ACCESS
Recombinant:
Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant Rabbit monoclonal anti-OGT HUABIO Cat# ET7107-17; RRID: AB_3070732 Mouse monoclonal anti- O-Linked N-Acetylglucosamine Abcam Cat# ab2739; RRID: AB_303264 Rabbit Polyclonal anti-beta Actin Servicebio Cat# GB11001; RRID: AB_2801259 Anti human Pancytokeratin Abcam Cat# ab234297; RRID:AB_ 2895302 Anti human CD4 Abcam Cat# ab133616; RRID: AB_2750883 Anti human CD8 Thermo Fisher Scientific Cat# MA1-80231; RRID: AB_929437 Anti human CD20 Cell Signaling Technology Cat# 48750S; RRID:AB_3107071 Anti human FOXP3 Cell Signaling Technology Cat# 98377; RRID: 2747370 Anti human CD68 Abcam Cat# ab280860; RRID: AB_2801637 Anti human CD163 Abcam Cat# ab182422; RRID: 2753196 Anti human CD86 Abcam Cat# ab220188; RRID: 3676334 Cyclin D1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1601-31; RRID: AB_3069614 Laminin beta 1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1703-14; RRID: AB_3070371 IL-18 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# HA721536; RRID: AB_3072652 AKT1/2/3 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1609-51; RRID: AB_2940862 Phospho-AKT (S473) Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1607-73; RRID: AB_2940863 PI 3 Kinase p85 alpha Recombinant Mouse Monoclonal Antibody HUABIO Cat# HA601206; RRID: AB_3071925 Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody Cell Signaling Technology Cat# 4228; RRID: 659940 Bacterial and virus strains Lentivirus: shRNA targeting OGT GenePharma Cat# D01001 Lentivirus: control shRNA GenePharma Cat# D03001 Lentivirus: OGT overexpression Generalbiol Cat# V1342936 Lentivirus: blank Generalbiol Cat# V1342935 Biological samples ESCC patient samples This paper N/A Chemicals, peptides, and recombinant proteins OSMI-1 Targetmol Cat# T16409 LY294002 Cayman Cat# 70920 D-Luciferin (potassium salt) Cayman chemical Cat# 14681 Puromycin Cayman chemical Cat# 13884 Critical commercial assays GP-transfect-Mate GenePharma Cat# G04008 Opal 7-Color Kit Akoya Biosciences N/A Superbrilliant® 6 min 1st Strand cDNA Synthesis Kit Zhongshi Gene Technology Cat# ZS-M14003 Superbrilliant® 2×ZAPA3G SYBR Green qPCR Mix Zhongshi Gene Technology Cat# ZS-M13002 Cell Counting Kit-8 MedChemExpress Cat# HY-K0301 (Continued on next page) e1 Cell Reports Medicine 7, 102650, March 17, 2026 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER PE Annexin V Apoptosis Detection Kit I BD Pharmingen Cat# 559763 PI/RNase Staining Buffer BD Pharmingen Cat# 554656 Deposited data Raw sequencing data This paper Genome Sequence Archive for Human (https:// cncb.ac.cn): HRA008846 TCGA datasets https://portal.gdc.cancer.gov N/A Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression Lin et al. 14 https://doi.org/10.1038/s41392-023-01710-2 Experimental models: Cell lines KYSE150 human ESCC cell line Haixing Biosciences TCH-C236 KYSE410 human ESCC cell line Haixing Biosciences TCH-C458 KYSE450 human ESCC cell line Servicebio STCC11902P KYSE30 human ESCC cell line Servicebio STCC11903P Experimental models: Organisms/strains Mouse: BALB/c-nu HFK Bioscience RRID:13001A Mouse: NOD SCID HFK Bioscience RRID:13002A Oligonucleotides Primers for RT-qPCR This paper N/A Recombinant DNA Plasmids and RNA interference sequences This paper N/A Software and algorithms GraphPad Prism 9 Graphpad software https://www.graphpad.com ImageJ https://imagej.net/ij/ R (v4.0.0) https://www.rproject.org GEPIA2 Zhang Lab 61 https://gepia2.cancer-pku.cn/ Seurat (v5.3.0) Hao et al. 62 https://satijalab.org/seurat/ edgeR (v4.6.2) Smyth et al. 63 https://bioconductor.org/packages/release/bioc/ html/edgeR.html clusterProfiler (V4.8.3) Yu et al. 64 N/A GeoMx NGS pipeline nanostring https://nanostring.com GeoMx DSP system nanostring https://nanostring.com ComplexHeatmap (v2.24.0) Gu et al. 65 https://bioconductor.org/packages/release/bioc/ html/ComplexHeatmap.html ggplot2 (v3.5.2) Pedersen et al. 66 https://tidyverse.r-universe.dev/ggplot2 Cibersort (v0.1.0) Alizadeh et al. 67 https://doi.org/10.1007/978-1-4939-7493-1_12 SpatialDecon (v1.18.0) Dandher et al. 68 https://doi.org/10.18129/B9.bioc.SpatialDecon ConsensusTME (v0.0.1) Miller et al. 69 https://doi.org/10.1158/0008-5472.CAN-18-3560 SCORPIUS (v1.0.9) Cannoodt et al. 70 https://github.com/rcannood/SCORPIUS CellChat (v1.5.0) Jin et al. 71 https://github.com/sqjin/CellChat STRING STRING Consortium 72 https://cn.string-db.org corrplot (v0.95) Wei et al. 73 https://github.com/taiyun/corrplot survival (v3.8-3) Therneau et al. 74 https://cran.r-project.org/web/packages/survival/ index.html survminer (v0.5.0) Kassambara et al. 75 https://cran.r-project.org/web/packages/ survminer/index.html Form (v2.4.4) Akoya Biosciences https://www.pubcompare.ai/product/ zzPiCZIBPBHhf-iFwRy1/ Cell Reports Medicine 7, 102650, March 17, 2026 e2 OPEN ACCESS
Analogues:
Enzyme-linked Immunosorbent Assay:
Cell Viability Assay:
SYBR Green Assay:
Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant Rabbit monoclonal anti-OGT HUABIO Cat# ET7107-17; RRID: AB_3070732 Mouse monoclonal anti- O-Linked N-Acetylglucosamine Abcam Cat# ab2739; RRID: AB_303264 Rabbit Polyclonal anti-beta Actin Servicebio Cat# GB11001; RRID: AB_2801259 Anti human Pancytokeratin Abcam Cat# ab234297; RRID:AB_ 2895302 Anti human CD4 Abcam Cat# ab133616; RRID: AB_2750883 Anti human CD8 Thermo Fisher Scientific Cat# MA1-80231; RRID: AB_929437 Anti human CD20 Cell Signaling Technology Cat# 48750S; RRID:AB_3107071 Anti human FOXP3 Cell Signaling Technology Cat# 98377; RRID: 2747370 Anti human CD68 Abcam Cat# ab280860; RRID: AB_2801637 Anti human CD163 Abcam Cat# ab182422; RRID: 2753196 Anti human CD86 Abcam Cat# ab220188; RRID: 3676334 Cyclin D1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1601-31; RRID: AB_3069614 Laminin beta 1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1703-14; RRID: AB_3070371 IL-18 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# HA721536; RRID: AB_3072652 AKT1/2/3 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1609-51; RRID: AB_2940862 Phospho-AKT (S473) Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1607-73; RRID: AB_2940863 PI 3 Kinase p85 alpha Recombinant Mouse Monoclonal Antibody HUABIO Cat# HA601206; RRID: AB_3071925 Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody Cell Signaling Technology Cat# 4228; RRID: 659940 Bacterial and virus strains Lentivirus: shRNA targeting OGT GenePharma Cat# D01001 Lentivirus: control shRNA GenePharma Cat# D03001 Lentivirus: OGT overexpression Generalbiol Cat# V1342936 Lentivirus: blank Generalbiol Cat# V1342935 Biological samples ESCC patient samples This paper N/A Chemicals, peptides, and recombinant proteins OSMI-1 Targetmol Cat# T16409 LY294002 Cayman Cat# 70920 D-Luciferin (potassium salt) Cayman chemical Cat# 14681 Puromycin Cayman chemical Cat# 13884 Critical commercial assays GP-transfect-Mate GenePharma Cat# G04008 Opal 7-Color Kit Akoya Biosciences N/A Superbrilliant® 6 min 1st Strand cDNA Synthesis Kit Zhongshi Gene Technology Cat# ZS-M14003 Superbrilliant® 2×ZAPA3G SYBR Green qPCR Mix Zhongshi Gene Technology Cat# ZS-M13002 Cell Counting Kit-8 MedChemExpress Cat# HY-K0301 (Continued on next page) e1 Cell Reports Medicine 7, 102650, March 17, 2026 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER PE Annexin V Apoptosis Detection Kit I BD Pharmingen Cat# 559763 PI/RNase Staining Buffer BD Pharmingen Cat# 554656 Deposited data Raw sequencing data This paper Genome Sequence Archive for Human (https:// cncb.ac.cn): HRA008846 TCGA datasets https://portal.gdc.cancer.gov N/A Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression Lin et al. 14 https://doi.org/10.1038/s41392-023-01710-2 Experimental models: Cell lines KYSE150 human ESCC cell line Haixing Biosciences TCH-C236 KYSE410 human ESCC cell line Haixing Biosciences TCH-C458 KYSE450 human ESCC cell line Servicebio STCC11902P KYSE30 human ESCC cell line Servicebio STCC11903P Experimental models: Organisms/strains Mouse: BALB/c-nu HFK Bioscience RRID:13001A Mouse: NOD SCID HFK Bioscience RRID:13002A Oligonucleotides Primers for RT-qPCR This paper N/A Recombinant DNA Plasmids and RNA interference sequences This paper N/A Software and algorithms GraphPad Prism 9 Graphpad software https://www.graphpad.com ImageJ https://imagej.net/ij/ R (v4.0.0) https://www.rproject.org GEPIA2 Zhang Lab 61 https://gepia2.cancer-pku.cn/ Seurat (v5.3.0) Hao et al. 62 https://satijalab.org/seurat/ edgeR (v4.6.2) Smyth et al. 63 https://bioconductor.org/packages/release/bioc/ html/edgeR.html clusterProfiler (V4.8.3) Yu et al. 64 N/A GeoMx NGS pipeline nanostring https://nanostring.com GeoMx DSP system nanostring https://nanostring.com ComplexHeatmap (v2.24.0) Gu et al. 65 https://bioconductor.org/packages/release/bioc/ html/ComplexHeatmap.html ggplot2 (v3.5.2) Pedersen et al. 66 https://tidyverse.r-universe.dev/ggplot2 Cibersort (v0.1.0) Alizadeh et al. 67 https://doi.org/10.1007/978-1-4939-7493-1_12 SpatialDecon (v1.18.0) Dandher et al. 68 https://doi.org/10.18129/B9.bioc.SpatialDecon ConsensusTME (v0.0.1) Miller et al. 69 https://doi.org/10.1158/0008-5472.CAN-18-3560 SCORPIUS (v1.0.9) Cannoodt et al. 70 https://github.com/rcannood/SCORPIUS CellChat (v1.5.0) Jin et al. 71 https://github.com/sqjin/CellChat STRING STRING Consortium 72 https://cn.string-db.org corrplot (v0.95) Wei et al. 73 https://github.com/taiyun/corrplot survival (v3.8-3) Therneau et al. 74 https://cran.r-project.org/web/packages/survival/ index.html survminer (v0.5.0) Kassambara et al. 75 https://cran.r-project.org/web/packages/ survminer/index.html Form (v2.4.4) Akoya Biosciences https://www.pubcompare.ai/product/ zzPiCZIBPBHhf-iFwRy1/ Cell Reports Medicine 7, 102650, March 17, 2026 e2 OPEN ACCESS
RNA sequencing:
shRNA:Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant Rabbit monoclonal anti-OGT HUABIO Cat# ET7107-17; RRID: AB_3070732 Mouse monoclonal anti- O-Linked N-Acetylglucosamine Abcam Cat# ab2739; RRID: AB_303264 Rabbit Polyclonal anti-beta Actin Servicebio Cat# GB11001; RRID: AB_2801259 Anti human Pancytokeratin Abcam Cat# ab234297; RRID:AB_ 2895302 Anti human CD4 Abcam Cat# ab133616; RRID: AB_2750883 Anti human CD8 Thermo Fisher Scientific Cat# MA1-80231; RRID: AB_929437 Anti human CD20 Cell Signaling Technology Cat# 48750S; RRID:AB_3107071 Anti human FOXP3 Cell Signaling Technology Cat# 98377; RRID: 2747370 Anti human CD68 Abcam Cat# ab280860; RRID: AB_2801637 Anti human CD163 Abcam Cat# ab182422; RRID: 2753196 Anti human CD86 Abcam Cat# ab220188; RRID: 3676334 Cyclin D1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1601-31; RRID: AB_3069614 Laminin beta 1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1703-14; RRID: AB_3070371 IL-18 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# HA721536; RRID: AB_3072652 AKT1/2/3 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1609-51; RRID: AB_2940862 Phospho-AKT (S473) Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1607-73; RRID: AB_2940863 PI 3 Kinase p85 alpha Recombinant Mouse Monoclonal Antibody HUABIO Cat# HA601206; RRID: AB_3071925 Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody Cell Signaling Technology Cat# 4228; RRID: 659940 Bacterial and virus strains Lentivirus: shRNA targeting OGT GenePharma Cat# D01001 Lentivirus: control shRNA GenePharma Cat# D03001 Lentivirus: OGT overexpression Generalbiol Cat# V1342936 Lentivirus: blank Generalbiol Cat# V1342935 Biological samples ESCC patient samples This paper N/A Chemicals, peptides, and recombinant proteins OSMI-1 Targetmol Cat# T16409 LY294002 Cayman Cat# 70920 D-Luciferin (potassium salt) Cayman chemical Cat# 14681 Puromycin Cayman chemical Cat# 13884 Critical commercial assays GP-transfect-Mate GenePharma Cat# G04008 Opal 7-Color Kit Akoya Biosciences N/A Superbrilliant® 6 min 1st Strand cDNA Synthesis Kit Zhongshi Gene Technology Cat# ZS-M14003 Superbrilliant® 2×ZAPA3G SYBR Green qPCR Mix Zhongshi Gene Technology Cat# ZS-M13002 Cell Counting Kit-8 MedChemExpress Cat# HY-K0301 (Continued on next page) e1 Cell Reports Medicine 7, 102650, March 17, 2026 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER PE Annexin V Apoptosis Detection Kit I BD Pharmingen Cat# 559763 PI/RNase Staining Buffer BD Pharmingen Cat# 554656 Deposited data Raw sequencing data This paper Genome Sequence Archive for Human (https:// cncb.ac.cn): HRA008846 TCGA datasets https://portal.gdc.cancer.gov N/A Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression Lin et al. 14 https://doi.org/10.1038/s41392-023-01710-2 Experimental models: Cell lines KYSE150 human ESCC cell line Haixing Biosciences TCH-C236 KYSE410 human ESCC cell line Haixing Biosciences TCH-C458 KYSE450 human ESCC cell line Servicebio STCC11902P KYSE30 human ESCC cell line Servicebio STCC11903P Experimental models: Organisms/strains Mouse: BALB/c-nu HFK Bioscience RRID:13001A Mouse: NOD SCID HFK Bioscience RRID:13002A Oligonucleotides Primers for RT-qPCR This paper N/A Recombinant DNA Plasmids and RNA interference sequences This paper N/A Software and algorithms GraphPad Prism 9 Graphpad software https://www.graphpad.com ImageJ https://imagej.net/ij/ R (v4.0.0) https://www.rproject.org GEPIA2 Zhang Lab 61 https://gepia2.cancer-pku.cn/ Seurat (v5.3.0) Hao et al. 62 https://satijalab.org/seurat/ edgeR (v4.6.2) Smyth et al. 63 https://bioconductor.org/packages/release/bioc/ html/edgeR.html clusterProfiler (V4.8.3) Yu et al. 64 N/A GeoMx NGS pipeline nanostring https://nanostring.com GeoMx DSP system nanostring https://nanostring.com ComplexHeatmap (v2.24.0) Gu et al. 65 https://bioconductor.org/packages/release/bioc/ html/ComplexHeatmap.html ggplot2 (v3.5.2) Pedersen et al. 66 https://tidyverse.r-universe.dev/ggplot2 Cibersort (v0.1.0) Alizadeh et al. 67 https://doi.org/10.1007/978-1-4939-7493-1_12 SpatialDecon (v1.18.0) Dandher et al. 68 https://doi.org/10.18129/B9.bioc.SpatialDecon ConsensusTME (v0.0.1) Miller et al. 69 https://doi.org/10.1158/0008-5472.CAN-18-3560 SCORPIUS (v1.0.9) Cannoodt et al. 70 https://github.com/rcannood/SCORPIUS CellChat (v1.5.0) Jin et al. 71 https://github.com/sqjin/CellChat STRING STRING Consortium 72 https://cn.string-db.org corrplot (v0.95) Wei et al. 73 https://github.com/taiyun/corrplot survival (v3.8-3) Therneau et al. 74 https://cran.r-project.org/web/packages/survival/ index.html survminer (v0.5.0) Kassambara et al. 75 https://cran.r-project.org/web/packages/ survminer/index.html Form (v2.4.4) Akoya Biosciences https://www.pubcompare.ai/product/ zzPiCZIBPBHhf-iFwRy1/ Cell Reports Medicine 7, 102650, March 17, 2026 e2 OPEN ACCESS
Control:Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant Rabbit monoclonal anti-OGT HUABIO Cat# ET7107-17; RRID: AB_3070732 Mouse monoclonal anti- O-Linked N-Acetylglucosamine Abcam Cat# ab2739; RRID: AB_303264 Rabbit Polyclonal anti-beta Actin Servicebio Cat# GB11001; RRID: AB_2801259 Anti human Pancytokeratin Abcam Cat# ab234297; RRID:AB_ 2895302 Anti human CD4 Abcam Cat# ab133616; RRID: AB_2750883 Anti human CD8 Thermo Fisher Scientific Cat# MA1-80231; RRID: AB_929437 Anti human CD20 Cell Signaling Technology Cat# 48750S; RRID:AB_3107071 Anti human FOXP3 Cell Signaling Technology Cat# 98377; RRID: 2747370 Anti human CD68 Abcam Cat# ab280860; RRID: AB_2801637 Anti human CD163 Abcam Cat# ab182422; RRID: 2753196 Anti human CD86 Abcam Cat# ab220188; RRID: 3676334 Cyclin D1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1601-31; RRID: AB_3069614 Laminin beta 1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1703-14; RRID: AB_3070371 IL-18 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# HA721536; RRID: AB_3072652 AKT1/2/3 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1609-51; RRID: AB_2940862 Phospho-AKT (S473) Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1607-73; RRID: AB_2940863 PI 3 Kinase p85 alpha Recombinant Mouse Monoclonal Antibody HUABIO Cat# HA601206; RRID: AB_3071925 Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody Cell Signaling Technology Cat# 4228; RRID: 659940 Bacterial and virus strains Lentivirus: shRNA targeting OGT GenePharma Cat# D01001 Lentivirus: control shRNA GenePharma Cat# D03001 Lentivirus: OGT overexpression Generalbiol Cat# V1342936 Lentivirus: blank Generalbiol Cat# V1342935 Biological samples ESCC patient samples This paper N/A Chemicals, peptides, and recombinant proteins OSMI-1 Targetmol Cat# T16409 LY294002 Cayman Cat# 70920 D-Luciferin (potassium salt) Cayman chemical Cat# 14681 Puromycin Cayman chemical Cat# 13884 Critical commercial assays GP-transfect-Mate GenePharma Cat# G04008 Opal 7-Color Kit Akoya Biosciences N/A Superbrilliant® 6 min 1st Strand cDNA Synthesis Kit Zhongshi Gene Technology Cat# ZS-M14003 Superbrilliant® 2×ZAPA3G SYBR Green qPCR Mix Zhongshi Gene Technology Cat# ZS-M13002 Cell Counting Kit-8 MedChemExpress Cat# HY-K0301 (Continued on next page) e1 Cell Reports Medicine 7, 102650, March 17, 2026 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER PE Annexin V Apoptosis Detection Kit I BD Pharmingen Cat# 559763 PI/RNase Staining Buffer BD Pharmingen Cat# 554656 Deposited data Raw sequencing data This paper Genome Sequence Archive for Human (https:// cncb.ac.cn): HRA008846 TCGA datasets https://portal.gdc.cancer.gov N/A Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression Lin et al. 14 https://doi.org/10.1038/s41392-023-01710-2 Experimental models: Cell lines KYSE150 human ESCC cell line Haixing Biosciences TCH-C236 KYSE410 human ESCC cell line Haixing Biosciences TCH-C458 KYSE450 human ESCC cell line Servicebio STCC11902P KYSE30 human ESCC cell line Servicebio STCC11903P Experimental models: Organisms/strains Mouse: BALB/c-nu HFK Bioscience RRID:13001A Mouse: NOD SCID HFK Bioscience RRID:13002A Oligonucleotides Primers for RT-qPCR This paper N/A Recombinant DNA Plasmids and RNA interference sequences This paper N/A Software and algorithms GraphPad Prism 9 Graphpad software https://www.graphpad.com ImageJ https://imagej.net/ij/ R (v4.0.0) https://www.rproject.org GEPIA2 Zhang Lab 61 https://gepia2.cancer-pku.cn/ Seurat (v5.3.0) Hao et al. 62 https://satijalab.org/seurat/ edgeR (v4.6.2) Smyth et al. 63 https://bioconductor.org/packages/release/bioc/ html/edgeR.html clusterProfiler (V4.8.3) Yu et al. 64 N/A GeoMx NGS pipeline nanostring https://nanostring.com GeoMx DSP system nanostring https://nanostring.com ComplexHeatmap (v2.24.0) Gu et al. 65 https://bioconductor.org/packages/release/bioc/ html/ComplexHeatmap.html ggplot2 (v3.5.2) Pedersen et al. 66 https://tidyverse.r-universe.dev/ggplot2 Cibersort (v0.1.0) Alizadeh et al. 67 https://doi.org/10.1007/978-1-4939-7493-1_12 SpatialDecon (v1.18.0) Dandher et al. 68 https://doi.org/10.18129/B9.bioc.SpatialDecon ConsensusTME (v0.0.1) Miller et al. 69 https://doi.org/10.1158/0008-5472.CAN-18-3560 SCORPIUS (v1.0.9) Cannoodt et al. 70 https://github.com/rcannood/SCORPIUS CellChat (v1.5.0) Jin et al. 71 https://github.com/sqjin/CellChat STRING STRING Consortium 72 https://cn.string-db.org corrplot (v0.95) Wei et al. 73 https://github.com/taiyun/corrplot survival (v3.8-3) Therneau et al. 74 https://cran.r-project.org/web/packages/survival/ index.html survminer (v0.5.0) Kassambara et al. 75 https://cran.r-project.org/web/packages/ survminer/index.html Form (v2.4.4) Akoya Biosciences https://www.pubcompare.ai/product/ zzPiCZIBPBHhf-iFwRy1/ Cell Reports Medicine 7, 102650, March 17, 2026 e2 OPEN ACCESS
Over Expression:Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant Rabbit monoclonal anti-OGT HUABIO Cat# ET7107-17; RRID: AB_3070732 Mouse monoclonal anti- O-Linked N-Acetylglucosamine Abcam Cat# ab2739; RRID: AB_303264 Rabbit Polyclonal anti-beta Actin Servicebio Cat# GB11001; RRID: AB_2801259 Anti human Pancytokeratin Abcam Cat# ab234297; RRID:AB_ 2895302 Anti human CD4 Abcam Cat# ab133616; RRID: AB_2750883 Anti human CD8 Thermo Fisher Scientific Cat# MA1-80231; RRID: AB_929437 Anti human CD20 Cell Signaling Technology Cat# 48750S; RRID:AB_3107071 Anti human FOXP3 Cell Signaling Technology Cat# 98377; RRID: 2747370 Anti human CD68 Abcam Cat# ab280860; RRID: AB_2801637 Anti human CD163 Abcam Cat# ab182422; RRID: 2753196 Anti human CD86 Abcam Cat# ab220188; RRID: 3676334 Cyclin D1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1601-31; RRID: AB_3069614 Laminin beta 1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1703-14; RRID: AB_3070371 IL-18 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# HA721536; RRID: AB_3072652 AKT1/2/3 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1609-51; RRID: AB_2940862 Phospho-AKT (S473) Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1607-73; RRID: AB_2940863 PI 3 Kinase p85 alpha Recombinant Mouse Monoclonal Antibody HUABIO Cat# HA601206; RRID: AB_3071925 Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody Cell Signaling Technology Cat# 4228; RRID: 659940 Bacterial and virus strains Lentivirus: shRNA targeting OGT GenePharma Cat# D01001 Lentivirus: control shRNA GenePharma Cat# D03001 Lentivirus: OGT overexpression Generalbiol Cat# V1342936 Lentivirus: blank Generalbiol Cat# V1342935 Biological samples ESCC patient samples This paper N/A Chemicals, peptides, and recombinant proteins OSMI-1 Targetmol Cat# T16409 LY294002 Cayman Cat# 70920 D-Luciferin (potassium salt) Cayman chemical Cat# 14681 Puromycin Cayman chemical Cat# 13884 Critical commercial assays GP-transfect-Mate GenePharma Cat# G04008 Opal 7-Color Kit Akoya Biosciences N/A Superbrilliant® 6 min 1st Strand cDNA Synthesis Kit Zhongshi Gene Technology Cat# ZS-M14003 Superbrilliant® 2×ZAPA3G SYBR Green qPCR Mix Zhongshi Gene Technology Cat# ZS-M13002 Cell Counting Kit-8 MedChemExpress Cat# HY-K0301 (Continued on next page) e1 Cell Reports Medicine 7, 102650, March 17, 2026 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER PE Annexin V Apoptosis Detection Kit I BD Pharmingen Cat# 559763 PI/RNase Staining Buffer BD Pharmingen Cat# 554656 Deposited data Raw sequencing data This paper Genome Sequence Archive for Human (https:// cncb.ac.cn): HRA008846 TCGA datasets https://portal.gdc.cancer.gov N/A Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression Lin et al. 14 https://doi.org/10.1038/s41392-023-01710-2 Experimental models: Cell lines KYSE150 human ESCC cell line Haixing Biosciences TCH-C236 KYSE410 human ESCC cell line Haixing Biosciences TCH-C458 KYSE450 human ESCC cell line Servicebio STCC11902P KYSE30 human ESCC cell line Servicebio STCC11903P Experimental models: Organisms/strains Mouse: BALB/c-nu HFK Bioscience RRID:13001A Mouse: NOD SCID HFK Bioscience RRID:13002A Oligonucleotides Primers for RT-qPCR This paper N/A Recombinant DNA Plasmids and RNA interference sequences This paper N/A Software and algorithms GraphPad Prism 9 Graphpad software https://www.graphpad.com ImageJ https://imagej.net/ij/ R (v4.0.0) https://www.rproject.org GEPIA2 Zhang Lab 61 https://gepia2.cancer-pku.cn/ Seurat (v5.3.0) Hao et al. 62 https://satijalab.org/seurat/ edgeR (v4.6.2) Smyth et al. 63 https://bioconductor.org/packages/release/bioc/ html/edgeR.html clusterProfiler (V4.8.3) Yu et al. 64 N/A GeoMx NGS pipeline nanostring https://nanostring.com GeoMx DSP system nanostring https://nanostring.com ComplexHeatmap (v2.24.0) Gu et al. 65 https://bioconductor.org/packages/release/bioc/ html/ComplexHeatmap.html ggplot2 (v3.5.2) Pedersen et al. 66 https://tidyverse.r-universe.dev/ggplot2 Cibersort (v0.1.0) Alizadeh et al. 67 https://doi.org/10.1007/978-1-4939-7493-1_12 SpatialDecon (v1.18.0) Dandher et al. 68 https://doi.org/10.18129/B9.bioc.SpatialDecon ConsensusTME (v0.0.1) Miller et al. 69 https://doi.org/10.1158/0008-5472.CAN-18-3560 SCORPIUS (v1.0.9) Cannoodt et al. 70 https://github.com/rcannood/SCORPIUS CellChat (v1.5.0) Jin et al. 71 https://github.com/sqjin/CellChat STRING STRING Consortium 72 https://cn.string-db.org corrplot (v0.95) Wei et al. 73 https://github.com/taiyun/corrplot survival (v3.8-3) Therneau et al. 74 https://cran.r-project.org/web/packages/survival/ index.html survminer (v0.5.0) Kassambara et al. 75 https://cran.r-project.org/web/packages/ survminer/index.html Form (v2.4.4) Akoya Biosciences https://www.pubcompare.ai/product/ zzPiCZIBPBHhf-iFwRy1/ Cell Reports Medicine 7, 102650, March 17, 2026 e2 OPEN ACCESS
cDNA Synthesis:Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant Rabbit monoclonal anti-OGT HUABIO Cat# ET7107-17; RRID: AB_3070732 Mouse monoclonal anti- O-Linked N-Acetylglucosamine Abcam Cat# ab2739; RRID: AB_303264 Rabbit Polyclonal anti-beta Actin Servicebio Cat# GB11001; RRID: AB_2801259 Anti human Pancytokeratin Abcam Cat# ab234297; RRID:AB_ 2895302 Anti human CD4 Abcam Cat# ab133616; RRID: AB_2750883 Anti human CD8 Thermo Fisher Scientific Cat# MA1-80231; RRID: AB_929437 Anti human CD20 Cell Signaling Technology Cat# 48750S; RRID:AB_3107071 Anti human FOXP3 Cell Signaling Technology Cat# 98377; RRID: 2747370 Anti human CD68 Abcam Cat# ab280860; RRID: AB_2801637 Anti human CD163 Abcam Cat# ab182422; RRID: 2753196 Anti human CD86 Abcam Cat# ab220188; RRID: 3676334 Cyclin D1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1601-31; RRID: AB_3069614 Laminin beta 1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1703-14; RRID: AB_3070371 IL-18 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# HA721536; RRID: AB_3072652 AKT1/2/3 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1609-51; RRID: AB_2940862 Phospho-AKT (S473) Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1607-73; RRID: AB_2940863 PI 3 Kinase p85 alpha Recombinant Mouse Monoclonal Antibody HUABIO Cat# HA601206; RRID: AB_3071925 Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody Cell Signaling Technology Cat# 4228; RRID: 659940 Bacterial and virus strains Lentivirus: shRNA targeting OGT GenePharma Cat# D01001 Lentivirus: control shRNA GenePharma Cat# D03001 Lentivirus: OGT overexpression Generalbiol Cat# V1342936 Lentivirus: blank Generalbiol Cat# V1342935 Biological samples ESCC patient samples This paper N/A Chemicals, peptides, and recombinant proteins OSMI-1 Targetmol Cat# T16409 LY294002 Cayman Cat# 70920 D-Luciferin (potassium salt) Cayman chemical Cat# 14681 Puromycin Cayman chemical Cat# 13884 Critical commercial assays GP-transfect-Mate GenePharma Cat# G04008 Opal 7-Color Kit Akoya Biosciences N/A Superbrilliant® 6 min 1st Strand cDNA Synthesis Kit Zhongshi Gene Technology Cat# ZS-M14003 Superbrilliant® 2×ZAPA3G SYBR Green qPCR Mix Zhongshi Gene Technology Cat# ZS-M13002 Cell Counting Kit-8 MedChemExpress Cat# HY-K0301 (Continued on next page) e1 Cell Reports Medicine 7, 102650, March 17, 2026 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER PE Annexin V Apoptosis Detection Kit I BD Pharmingen Cat# 559763 PI/RNase Staining Buffer BD Pharmingen Cat# 554656 Deposited data Raw sequencing data This paper Genome Sequence Archive for Human (https:// cncb.ac.cn): HRA008846 TCGA datasets https://portal.gdc.cancer.gov N/A Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression Lin et al. 14 https://doi.org/10.1038/s41392-023-01710-2 Experimental models: Cell lines KYSE150 human ESCC cell line Haixing Biosciences TCH-C236 KYSE410 human ESCC cell line Haixing Biosciences TCH-C458 KYSE450 human ESCC cell line Servicebio STCC11902P KYSE30 human ESCC cell line Servicebio STCC11903P Experimental models: Organisms/strains Mouse: BALB/c-nu HFK Bioscience RRID:13001A Mouse: NOD SCID HFK Bioscience RRID:13002A Oligonucleotides Primers for RT-qPCR This paper N/A Recombinant DNA Plasmids and RNA interference sequences This paper N/A Software and algorithms GraphPad Prism 9 Graphpad software https://www.graphpad.com ImageJ https://imagej.net/ij/ R (v4.0.0) https://www.rproject.org GEPIA2 Zhang Lab 61 https://gepia2.cancer-pku.cn/ Seurat (v5.3.0) Hao et al. 62 https://satijalab.org/seurat/ edgeR (v4.6.2) Smyth et al. 63 https://bioconductor.org/packages/release/bioc/ html/edgeR.html clusterProfiler (V4.8.3) Yu et al. 64 N/A GeoMx NGS pipeline nanostring https://nanostring.com GeoMx DSP system nanostring https://nanostring.com ComplexHeatmap (v2.24.0) Gu et al. 65 https://bioconductor.org/packages/release/bioc/ html/ComplexHeatmap.html ggplot2 (v3.5.2) Pedersen et al. 66 https://tidyverse.r-universe.dev/ggplot2 Cibersort (v0.1.0) Alizadeh et al. 67 https://doi.org/10.1007/978-1-4939-7493-1_12 SpatialDecon (v1.18.0) Dandher et al. 68 https://doi.org/10.18129/B9.bioc.SpatialDecon ConsensusTME (v0.0.1) Miller et al. 69 https://doi.org/10.1158/0008-5472.CAN-18-3560 SCORPIUS (v1.0.9) Cannoodt et al. 70 https://github.com/rcannood/SCORPIUS CellChat (v1.5.0) Jin et al. 71 https://github.com/sqjin/CellChat STRING STRING Consortium 72 https://cn.string-db.org corrplot (v0.95) Wei et al. 73 https://github.com/taiyun/corrplot survival (v3.8-3) Therneau et al. 74 https://cran.r-project.org/web/packages/survival/ index.html survminer (v0.5.0) Kassambara et al. 75 https://cran.r-project.org/web/packages/ survminer/index.html Form (v2.4.4) Akoya Biosciences https://www.pubcompare.ai/product/ zzPiCZIBPBHhf-iFwRy1/ Cell Reports Medicine 7, 102650, March 17, 2026 e2 OPEN ACCESS
Real-time Polymerase Chain Reaction:Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant Rabbit monoclonal anti-OGT HUABIO Cat# ET7107-17; RRID: AB_3070732 Mouse monoclonal anti- O-Linked N-Acetylglucosamine Abcam Cat# ab2739; RRID: AB_303264 Rabbit Polyclonal anti-beta Actin Servicebio Cat# GB11001; RRID: AB_2801259 Anti human Pancytokeratin Abcam Cat# ab234297; RRID:AB_ 2895302 Anti human CD4 Abcam Cat# ab133616; RRID: AB_2750883 Anti human CD8 Thermo Fisher Scientific Cat# MA1-80231; RRID: AB_929437 Anti human CD20 Cell Signaling Technology Cat# 48750S; RRID:AB_3107071 Anti human FOXP3 Cell Signaling Technology Cat# 98377; RRID: 2747370 Anti human CD68 Abcam Cat# ab280860; RRID: AB_2801637 Anti human CD163 Abcam Cat# ab182422; RRID: 2753196 Anti human CD86 Abcam Cat# ab220188; RRID: 3676334 Cyclin D1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1601-31; RRID: AB_3069614 Laminin beta 1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1703-14; RRID: AB_3070371 IL-18 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# HA721536; RRID: AB_3072652 AKT1/2/3 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1609-51; RRID: AB_2940862 Phospho-AKT (S473) Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1607-73; RRID: AB_2940863 PI 3 Kinase p85 alpha Recombinant Mouse Monoclonal Antibody HUABIO Cat# HA601206; RRID: AB_3071925 Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody Cell Signaling Technology Cat# 4228; RRID: 659940 Bacterial and virus strains Lentivirus: shRNA targeting OGT GenePharma Cat# D01001 Lentivirus: control shRNA GenePharma Cat# D03001 Lentivirus: OGT overexpression Generalbiol Cat# V1342936 Lentivirus: blank Generalbiol Cat# V1342935 Biological samples ESCC patient samples This paper N/A Chemicals, peptides, and recombinant proteins OSMI-1 Targetmol Cat# T16409 LY294002 Cayman Cat# 70920 D-Luciferin (potassium salt) Cayman chemical Cat# 14681 Puromycin Cayman chemical Cat# 13884 Critical commercial assays GP-transfect-Mate GenePharma Cat# G04008 Opal 7-Color Kit Akoya Biosciences N/A Superbrilliant® 6 min 1st Strand cDNA Synthesis Kit Zhongshi Gene Technology Cat# ZS-M14003 Superbrilliant® 2×ZAPA3G SYBR Green qPCR Mix Zhongshi Gene Technology Cat# ZS-M13002 Cell Counting Kit-8 MedChemExpress Cat# HY-K0301 (Continued on next page) e1 Cell Reports Medicine 7, 102650, March 17, 2026 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER PE Annexin V Apoptosis Detection Kit I BD Pharmingen Cat# 559763 PI/RNase Staining Buffer BD Pharmingen Cat# 554656 Deposited data Raw sequencing data This paper Genome Sequence Archive for Human (https:// cncb.ac.cn): HRA008846 TCGA datasets https://portal.gdc.cancer.gov N/A Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression Lin et al. 14 https://doi.org/10.1038/s41392-023-01710-2 Experimental models: Cell lines KYSE150 human ESCC cell line Haixing Biosciences TCH-C236 KYSE410 human ESCC cell line Haixing Biosciences TCH-C458 KYSE450 human ESCC cell line Servicebio STCC11902P KYSE30 human ESCC cell line Servicebio STCC11903P Experimental models: Organisms/strains Mouse: BALB/c-nu HFK Bioscience RRID:13001A Mouse: NOD SCID HFK Bioscience RRID:13002A Oligonucleotides Primers for RT-qPCR This paper N/A Recombinant DNA Plasmids and RNA interference sequences This paper N/A Software and algorithms GraphPad Prism 9 Graphpad software https://www.graphpad.com ImageJ https://imagej.net/ij/ R (v4.0.0) https://www.rproject.org GEPIA2 Zhang Lab 61 https://gepia2.cancer-pku.cn/ Seurat (v5.3.0) Hao et al. 62 https://satijalab.org/seurat/ edgeR (v4.6.2) Smyth et al. 63 https://bioconductor.org/packages/release/bioc/ html/edgeR.html clusterProfiler (V4.8.3) Yu et al. 64 N/A GeoMx NGS pipeline nanostring https://nanostring.com GeoMx DSP system nanostring https://nanostring.com ComplexHeatmap (v2.24.0) Gu et al. 65 https://bioconductor.org/packages/release/bioc/ html/ComplexHeatmap.html ggplot2 (v3.5.2) Pedersen et al. 66 https://tidyverse.r-universe.dev/ggplot2 Cibersort (v0.1.0) Alizadeh et al. 67 https://doi.org/10.1007/978-1-4939-7493-1_12 SpatialDecon (v1.18.0) Dandher et al. 68 https://doi.org/10.18129/B9.bioc.SpatialDecon ConsensusTME (v0.0.1) Miller et al. 69 https://doi.org/10.1158/0008-5472.CAN-18-3560 SCORPIUS (v1.0.9) Cannoodt et al. 70 https://github.com/rcannood/SCORPIUS CellChat (v1.5.0) Jin et al. 71 https://github.com/sqjin/CellChat STRING STRING Consortium 72 https://cn.string-db.org corrplot (v0.95) Wei et al. 73 https://github.com/taiyun/corrplot survival (v3.8-3) Therneau et al. 74 https://cran.r-project.org/web/packages/survival/ index.html survminer (v0.5.0) Kassambara et al. 75 https://cran.r-project.org/web/packages/ survminer/index.html Form (v2.4.4) Akoya Biosciences https://www.pubcompare.ai/product/ zzPiCZIBPBHhf-iFwRy1/ Cell Reports Medicine 7, 102650, March 17, 2026 e2 OPEN ACCESS
CCK-8 Assay:Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant Rabbit monoclonal anti-OGT HUABIO Cat# ET7107-17; RRID: AB_3070732 Mouse monoclonal anti- O-Linked N-Acetylglucosamine Abcam Cat# ab2739; RRID: AB_303264 Rabbit Polyclonal anti-beta Actin Servicebio Cat# GB11001; RRID: AB_2801259 Anti human Pancytokeratin Abcam Cat# ab234297; RRID:AB_ 2895302 Anti human CD4 Abcam Cat# ab133616; RRID: AB_2750883 Anti human CD8 Thermo Fisher Scientific Cat# MA1-80231; RRID: AB_929437 Anti human CD20 Cell Signaling Technology Cat# 48750S; RRID:AB_3107071 Anti human FOXP3 Cell Signaling Technology Cat# 98377; RRID: 2747370 Anti human CD68 Abcam Cat# ab280860; RRID: AB_2801637 Anti human CD163 Abcam Cat# ab182422; RRID: 2753196 Anti human CD86 Abcam Cat# ab220188; RRID: 3676334 Cyclin D1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1601-31; RRID: AB_3069614 Laminin beta 1 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1703-14; RRID: AB_3070371 IL-18 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# HA721536; RRID: AB_3072652 AKT1/2/3 Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1609-51; RRID: AB_2940862 Phospho-AKT (S473) Recombinant Rabbit Monoclonal Antibody HUABIO Cat# ET1607-73; RRID: AB_2940863 PI 3 Kinase p85 alpha Recombinant Mouse Monoclonal Antibody HUABIO Cat# HA601206; RRID: AB_3071925 Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody Cell Signaling Technology Cat# 4228; RRID: 659940 Bacterial and virus strains Lentivirus: shRNA targeting OGT GenePharma Cat# D01001 Lentivirus: control shRNA GenePharma Cat# D03001 Lentivirus: OGT overexpression Generalbiol Cat# V1342936 Lentivirus: blank Generalbiol Cat# V1342935 Biological samples ESCC patient samples This paper N/A Chemicals, peptides, and recombinant proteins OSMI-1 Targetmol Cat# T16409 LY294002 Cayman Cat# 70920 D-Luciferin (potassium salt) Cayman chemical Cat# 14681 Puromycin Cayman chemical Cat# 13884 Critical commercial assays GP-transfect-Mate GenePharma Cat# G04008 Opal 7-Color Kit Akoya Biosciences N/A Superbrilliant® 6 min 1st Strand cDNA Synthesis Kit Zhongshi Gene Technology Cat# ZS-M14003 Superbrilliant® 2×ZAPA3G SYBR Green qPCR Mix Zhongshi Gene Technology Cat# ZS-M13002 Cell Counting Kit-8 MedChemExpress Cat# HY-K0301 (Continued on next page) e1 Cell Reports Medicine 7, 102650, March 17, 2026 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER PE Annexin V Apoptosis Detection Kit I BD Pharmingen Cat# 559763 PI/RNase Staining Buffer BD Pharmingen Cat# 554656 Deposited data Raw sequencing data This paper Genome Sequence Archive for Human (https:// cncb.ac.cn): HRA008846 TCGA datasets https://portal.gdc.cancer.gov N/A Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression Lin et al. 14 https://doi.org/10.1038/s41392-023-01710-2 Experimental models: Cell lines KYSE150 human ESCC cell line Haixing Biosciences TCH-C236 KYSE410 human ESCC cell line Haixing Biosciences TCH-C458 KYSE450 human ESCC cell line Servicebio STCC11902P KYSE30 human ESCC cell line Servicebio STCC11903P Experimental models: Organisms/strains Mouse: BALB/c-nu HFK Bioscience RRID:13001A Mouse: NOD SCID HFK Bioscience RRID:13002A Oligonucleotides Primers for RT-qPCR This paper N/A Recombinant DNA Plasmids and RNA interference sequences This paper N/A Software and algorithms GraphPad Prism 9 Graphpad software https://www.graphpad.com ImageJ https://imagej.net/ij/ R (v4.0.0) https://www.rproject.org GEPIA2 Zhang Lab 61 https://gepia2.cancer-pku.cn/ Seurat (v5.3.0) Hao et al. 62 https://satijalab.org/seurat/ edgeR (v4.6.2) Smyth et al. 63 https://bioconductor.org/packages/release/bioc/ html/edgeR.html clusterProfiler (V4.8.3) Yu et al. 64 N/A GeoMx NGS pipeline nanostring https://nanostring.com GeoMx DSP system nanostring https://nanostring.com ComplexHeatmap (v2.24.0) Gu et al. 65 https://bioconductor.org/packages/release/bioc/ html/ComplexHeatmap.html ggplot2 (v3.5.2) Pedersen et al. 66 https://tidyverse.r-universe.dev/ggplot2 Cibersort (v0.1.0) Alizadeh et al. 67 https://doi.org/10.1007/978-1-4939-7493-1_12 SpatialDecon (v1.18.0) Dandher et al. 68 https://doi.org/10.18129/B9.bioc.SpatialDecon ConsensusTME (v0.0.1) Miller et al. 69 https://doi.org/10.1158/0008-5472.CAN-18-3560 SCORPIUS (v1.0.9) Cannoodt et al. 70 https://github.com/rcannood/SCORPIUS CellChat (v1.5.0) Jin et al. 71 https://github.com/sqjin/CellChat STRING STRING Consortium 72 https://cn.string-db.org corrplot (v0.95) Wei et al. 73 https://github.com/taiyun/corrplot survival (v3.8-3) Therneau et al. 74 https://cran.r-project.org/web/packages/survival/ index.html survminer (v0.5.0) Kassambara et al. 75 https://cran.r-project.org/web/packages/ survminer/index.html Form (v2.4.4) Akoya Biosciences https://www.pubcompare.ai/product/ zzPiCZIBPBHhf-iFwRy1/ Cell Reports Medicine 7, 102650, March 17, 2026 e2 OPEN ACCESS
other:Article Title: PTBP1 enforces ATR-CHK1 signaling determining the potency of CDC7 inhibitors.
Article Snippet: Antibodies Anti-53BP1 rabbit polyclonal Novus Biologicals Cat# NB100-304; RRID: AB_10003037 Anti-ATR pT1989 rabbit polyclonal GeneTex Cat# GTX128145; RRID:AB_2687562 Anti-beta-Tubulin mouse monoclonal Millipore Cat# 05-661; RRID: AB_309885 Anti-BrdU (BU1/75 (ICR1)) rat monoclonal ThermoFisher Cat# MA1-82088; RRID: AB_927214 Anti-BrdU (B44) IgG1 mouse monoclonal BD biosciences Cat# 347580; RRID: AB_10015219 Anti-CHK1 pS345 (133D3) rabbit monoclonal Cell Signaling Technology Cat# 2348; RRID:AB_331212 Anti-CHK1 (G4) mouse monoclonal Santa Cruz Biotechnology Cat# SC-8408; RRID:AB_627257 Anti-MCM2 rabbit polyclonal in house previously described (Rainey et al. 2017)26 N/A Anti-MCM2 pS40/41 rabbit polyclonal in house previously described (Rainey et al. 2017)26 N/A Anti-hnRNP I (Anti-PTBP1) (SH54) mouse monoclonal Santa Cruz Biotechnology Cat# SC-56701; RRID:AB_783822 Anti-hnRNP I (Anti-PTBP1) (A-4) mouse monoclonal Santa Cruz Biotechnology Cat# SC-515282 Anti-RPA2 (Ab-3) mouse monoclonal Calbiochem Cat# NA19L; RRID:AB_565123 Anti-RAD51AP1 rabbit polyclonal Sigma-Aldrich/Merck Cat# HPA051499; RRID:AB_2681508 Anti-RAD51 rabbit polyclonal Santa Cruz Biotechnology Cat# SC-8349; RRID:AB_2253533 IRDye 800CW goat anti-rabbit IgG antibody LI-COR Biosciences Cat# 926-32211; RRID:AB_621843 IRDye 800CW goat anti-mouse IgG antibody LI-COR Biosciences Cat# 926-32210; RRID:AB_621842 Chicken anti-rat Alexa Fluor 488 ThermoFisher Cat# A21470; RRID: AB_2535873 Goat anti-rabbit IgG Alexa Fluor 546 ThermoFisher Cat# A11010; RRID AB_2534077 Goat anti-mouse IgG Alexa Fluor 546 ThermoFisher Cat# A11003; RRID: AB_2534071 Goat anti-mouse IgG1 Alexa Fluor 546 ThermoFisher Cat# A21123; RRID:AB_2535765
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