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cdna microarray genechip human genome hg-u133a  (Thermo Fisher)


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    Thermo Fisher cdna microarray genechip human genome hg-u133a
    Cdna Microarray Genechip Human Genome Hg U133a, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/human+cdna+microarray/seebluetm+plus2+pre+stained+protein+standard/pmc12070984-99-0-7
    Average 90 stars, based on 1 article reviews
    cdna microarray genechip human genome hg-u133a - by Bioz Stars, 2026-11
    90/100 stars

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    Microarray:

    Article Title: UV‐A Radiation Impairs Sebaceous‐Gland‐Related Skin Barrier Function by Inducing Inflammation and Altering Intracellular Sebum‐Like Lipid Composition
    Article Snippet: Total RNA was extracted using a NucleoSpin Plus XS kit (Macherey‐Nagel GmbH & Co. KG, Düren, Germany). .. For DNA microarray analysis, 250 ng of total RNA was processed using the Clariom S Array, human (Thermo Fisher Scientific), following the manufacturer's protocol. .. For reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR), total RNA was reverse‐transcribed into cDNA using SuperScript IV VILO Master Mix (Thermo Fisher Scientific), and TaqMan Universal Master Mix II, no UNG (Thermo Fisher Scientific), was used for qPCR reactions.

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Article Title: Deoxy-cytidine or uridine derivatives for use in cancer therapies
    Article Snippet: .. Microarray Method A comprises the following steps: 1) Extracting RNA from cancer/tumour cells of interest, said extraction preferably being performed using a Norgen Total RNA Purification kit (Norgen Biotek Cat nr. 17200); 2) Preparing Poly(A)+ RNA from the extracted RNA, preferably using a MEGApure kit according to the manufacturer's instructions (Ambion); 3) Preparing complementary DNA (cDNA) from the Poly(A)+ RNA by treatment with reverse transcriptase, i.e. performing reverse transcription; 4) Fragmenting the cDNA using TdT (terminal deoxynucleotidyl transferase); 5) Biotinylating the cDNA fragments using the GeneChip WT Terminal labelling kit (Affymetrix); 6 Repeating steps 1 to 5 with a reference cell line, wherein said reference cell line is MDA-MB-231; 7) Hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 5 to a first DNA microarray at 45° C. for 16 hours, and hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 6, to a DNA microarray at 45° C. for 16 hours, preferably wherein said microarrays are Affymetrix GeneChip Human Gene 2.0 ST Arrays (Applied Biosystems); 8) Washing and staining the hybridized microarrays, preferably in the Affymetrix GeneChip Fluidics Station 450 (Applied Biosystems); 9) Scanning said stained microarrays with the Affymetrix GeneChip Scanner 3000 7G utilising the Affymetrix GeneChip Command Console® software to produce raw data signal values in the form of CEL files; 10) Normalizing the CEL files to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the Affymetrix software package (version 1.36.1), preferably as described in R. A. Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. ..

    Article Title: Identification of lncRNA ZNF252P-AS1 as a novel diagnostic and prognostic biomarker for breast cancer patients: An integrated bioinformatics and experimental analysis.
    Article Snippet: Background: Long non-coding RNAs (lncRNAs) have emerged as useful diagnostic and prognostic markers as well as therapeutic targets in cancer.. Dysregulated levels of lncRNAs have been described in various cancers including breast cancer (BC).. Our study aims to screen novel lncRNAs involved in BC and investigate any possible role in helping diagnosis and determining prognosis of BC patients.

    Article Title: UV-A Radiation Impairs Sebaceous-Gland-Related Skin Barrier Function by Inducing Inflammation and Altering Intracellular Sebum-Like Lipid Composition.
    Article Snippet: Total RNA was extracted using a NucleoSpin Plus XS kit (Macherey- Nagel GmbH & Co. KG, Düren, Germany). .. For DNA microarray analysis, 250 ng of total RNA was processed using the Clariom S Array, human (Thermo Fisher Scientific), following the manufacturer's protocol. .. For reverse transcription- quantitative polymerase chain reaction (RT- qPCR), total RNA was reverse- transcribed into cDNA using SuperScript IV VILO Master Mix (Thermo Fisher Scientific), and TaqMan Universal Master Mix II, no UNG (Thermo Fisher Scientific), was used for qPCR reactions.

    cDNA Synthesis:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    SYBR Green Assay:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    DNA Extraction:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Bicinchoninic Acid Protein Assay:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Enzyme-linked Immunosorbent Assay:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    ROS Assay:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Activity Assay:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Purification:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Article Title: Deoxy-cytidine or uridine derivatives for use in cancer therapies
    Article Snippet: .. Microarray Method A comprises the following steps: 1) Extracting RNA from cancer/tumour cells of interest, said extraction preferably being performed using a Norgen Total RNA Purification kit (Norgen Biotek Cat nr. 17200); 2) Preparing Poly(A)+ RNA from the extracted RNA, preferably using a MEGApure kit according to the manufacturer's instructions (Ambion); 3) Preparing complementary DNA (cDNA) from the Poly(A)+ RNA by treatment with reverse transcriptase, i.e. performing reverse transcription; 4) Fragmenting the cDNA using TdT (terminal deoxynucleotidyl transferase); 5) Biotinylating the cDNA fragments using the GeneChip WT Terminal labelling kit (Affymetrix); 6 Repeating steps 1 to 5 with a reference cell line, wherein said reference cell line is MDA-MB-231; 7) Hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 5 to a first DNA microarray at 45° C. for 16 hours, and hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 6, to a DNA microarray at 45° C. for 16 hours, preferably wherein said microarrays are Affymetrix GeneChip Human Gene 2.0 ST Arrays (Applied Biosystems); 8) Washing and staining the hybridized microarrays, preferably in the Affymetrix GeneChip Fluidics Station 450 (Applied Biosystems); 9) Scanning said stained microarrays with the Affymetrix GeneChip Scanner 3000 7G utilising the Affymetrix GeneChip Command Console® software to produce raw data signal values in the form of CEL files; 10) Normalizing the CEL files to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the Affymetrix software package (version 1.36.1), preferably as described in R. A. Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. ..

    RNA Sequencing:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Article Title: Identification of lncRNA ZNF252P-AS1 as a novel diagnostic and prognostic biomarker for breast cancer patients: An integrated bioinformatics and experimental analysis.
    Article Snippet: Background: Long non-coding RNAs (lncRNAs) have emerged as useful diagnostic and prognostic markers as well as therapeutic targets in cancer.. Dysregulated levels of lncRNAs have been described in various cancers including breast cancer (BC).. Our study aims to screen novel lncRNAs involved in BC and investigate any possible role in helping diagnosis and determining prognosis of BC patients.

    other:

    Article Title: Targeting PI3Kδ suppresses pancreatic cancer by dual disruption of fibrosis and immune evasion.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Amersham ECL Anti-rabbit IgG, HRP-linked whole Ab GE Healthcare Life Sciences Cat#NA934, RRID:AB_772206 Alexa Fluor 488 donkey Anti-rabbit (IHC: 1/500) Thermo Scientific Cat#A21206, RRID:AB_141708 Alexa Fluor 594 donkey Anti-rabbit (IHC: 1/500) Thermo Scientific Cat#A21207, RRID:AB_141637 Alexa Fluor 488 goat Anti-mouse (IHC: 1/500) Thermo Scientific Cat#A21121, RRID:AB_141514 Alexa Fluor 594 goat Anti-mouse (IHC: 1/500) Thermo Scientific Cat#A21135, RRID:AB_2535774 Alexa Fluor 488 goat Anti-rat (IHC: 1/500) Thermo Scientific Cat#A11006, RRID:AB_141373 Alexa Fluor 594 goat Anti-rat (IHC: 1/500) Thermo Scientific Cat#A11007, RRID:AB_141374 ImmPRESS® HRP Anti-rabbit IgG (Peroxidase) Vector labs Cat#MP-7401, RRID:AB_2336529 ImmPRESS® HRP Anti-mouse IgG (Peroxidase) Vector labs Cat#MP-7402, RRID:AB_2336528 ImmPRESS® HRP Anti-rat IgG (Peroxidase) Vector labs Cat#MP-7444, RRID:AB_2336530 Bacterial and virus strains One Shot Stbl3 Chemically Competent E. coli Thermo Scientific Cat#C737303 Biological samples Human tumor tissue microarray (TMA) University of Bern, Institute of Pathology, Translational Research Unit N/A Chemicals, peptides, and recombinant proteins TransIT®-293 Transfection Reagent Mirus Bio Cat#MIR2705 Immobilon Forte Western HRP Substrate Millipore Cat#WBUF0500 Methyl Green Vector Labs Cat#H-3402 Annexin V-Atto 633 In house N/A Propidium Iodide (PI) Invitrogen Cat#P3566 Puromycin Gibco Cat#A11138-03 Cambritaxestat Provided by iOnctura N/A Roginolisib Provided by iOnctura N/A LPA 18:1 Sigma-Aldrich Cat#857130P DAB+ solution Dako Cat#Κ3467 M.O.M.® (Mouse on Mouse) Blocking Reagent Vector labs Cat#MKB-2213 FastSybr© green Thermo Scientific Cat#4367659 Doxycycline (1 μg/mL) Thermo Scientific Cat# BP2653 ReadyProbesTM 2.5% Normal Horse Serum Thermo Scientific Cat#R37625 Critical commercial assays KAPA HotStart Mouse Gentotyping Kit Kapa Biosystems Cat#KK7352 Proteome Profiler Human XL Cytokine Array Kit R&D Systems Cat#ARY022B Human IL-8/CXCL8 ELISA Kit - Quantikine R&D Systems Cat#D8000C cDNA Synthesis Kit Thermo Scientific Cat# K1622 Deposited data Manuscript figure source data Zenodo https://doi.org/10.5281/zenodo.18607846 Lipidomics data National Metabolomics Data Repository (NMDR) https://doi.org/10.21228/M8C268 (Continued on next page) 18 Cell Reports 45, 117188, April 28, 2026

    Extraction:

    Article Title: Deoxy-cytidine or uridine derivatives for use in cancer therapies
    Article Snippet: .. Microarray Method A comprises the following steps: 1) Extracting RNA from cancer/tumour cells of interest, said extraction preferably being performed using a Norgen Total RNA Purification kit (Norgen Biotek Cat nr. 17200); 2) Preparing Poly(A)+ RNA from the extracted RNA, preferably using a MEGApure kit according to the manufacturer's instructions (Ambion); 3) Preparing complementary DNA (cDNA) from the Poly(A)+ RNA by treatment with reverse transcriptase, i.e. performing reverse transcription; 4) Fragmenting the cDNA using TdT (terminal deoxynucleotidyl transferase); 5) Biotinylating the cDNA fragments using the GeneChip WT Terminal labelling kit (Affymetrix); 6 Repeating steps 1 to 5 with a reference cell line, wherein said reference cell line is MDA-MB-231; 7) Hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 5 to a first DNA microarray at 45° C. for 16 hours, and hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 6, to a DNA microarray at 45° C. for 16 hours, preferably wherein said microarrays are Affymetrix GeneChip Human Gene 2.0 ST Arrays (Applied Biosystems); 8) Washing and staining the hybridized microarrays, preferably in the Affymetrix GeneChip Fluidics Station 450 (Applied Biosystems); 9) Scanning said stained microarrays with the Affymetrix GeneChip Scanner 3000 7G utilising the Affymetrix GeneChip Command Console® software to produce raw data signal values in the form of CEL files; 10) Normalizing the CEL files to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the Affymetrix software package (version 1.36.1), preferably as described in R. A. Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. ..

    Reverse Transcription:

    Article Title: Deoxy-cytidine or uridine derivatives for use in cancer therapies
    Article Snippet: .. Microarray Method A comprises the following steps: 1) Extracting RNA from cancer/tumour cells of interest, said extraction preferably being performed using a Norgen Total RNA Purification kit (Norgen Biotek Cat nr. 17200); 2) Preparing Poly(A)+ RNA from the extracted RNA, preferably using a MEGApure kit according to the manufacturer's instructions (Ambion); 3) Preparing complementary DNA (cDNA) from the Poly(A)+ RNA by treatment with reverse transcriptase, i.e. performing reverse transcription; 4) Fragmenting the cDNA using TdT (terminal deoxynucleotidyl transferase); 5) Biotinylating the cDNA fragments using the GeneChip WT Terminal labelling kit (Affymetrix); 6 Repeating steps 1 to 5 with a reference cell line, wherein said reference cell line is MDA-MB-231; 7) Hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 5 to a first DNA microarray at 45° C. for 16 hours, and hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 6, to a DNA microarray at 45° C. for 16 hours, preferably wherein said microarrays are Affymetrix GeneChip Human Gene 2.0 ST Arrays (Applied Biosystems); 8) Washing and staining the hybridized microarrays, preferably in the Affymetrix GeneChip Fluidics Station 450 (Applied Biosystems); 9) Scanning said stained microarrays with the Affymetrix GeneChip Scanner 3000 7G utilising the Affymetrix GeneChip Command Console® software to produce raw data signal values in the form of CEL files; 10) Normalizing the CEL files to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the Affymetrix software package (version 1.36.1), preferably as described in R. A. Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. ..

    Multiple Displacement Amplification:

    Article Title: Deoxy-cytidine or uridine derivatives for use in cancer therapies
    Article Snippet: .. Microarray Method A comprises the following steps: 1) Extracting RNA from cancer/tumour cells of interest, said extraction preferably being performed using a Norgen Total RNA Purification kit (Norgen Biotek Cat nr. 17200); 2) Preparing Poly(A)+ RNA from the extracted RNA, preferably using a MEGApure kit according to the manufacturer's instructions (Ambion); 3) Preparing complementary DNA (cDNA) from the Poly(A)+ RNA by treatment with reverse transcriptase, i.e. performing reverse transcription; 4) Fragmenting the cDNA using TdT (terminal deoxynucleotidyl transferase); 5) Biotinylating the cDNA fragments using the GeneChip WT Terminal labelling kit (Affymetrix); 6 Repeating steps 1 to 5 with a reference cell line, wherein said reference cell line is MDA-MB-231; 7) Hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 5 to a first DNA microarray at 45° C. for 16 hours, and hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 6, to a DNA microarray at 45° C. for 16 hours, preferably wherein said microarrays are Affymetrix GeneChip Human Gene 2.0 ST Arrays (Applied Biosystems); 8) Washing and staining the hybridized microarrays, preferably in the Affymetrix GeneChip Fluidics Station 450 (Applied Biosystems); 9) Scanning said stained microarrays with the Affymetrix GeneChip Scanner 3000 7G utilising the Affymetrix GeneChip Command Console® software to produce raw data signal values in the form of CEL files; 10) Normalizing the CEL files to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the Affymetrix software package (version 1.36.1), preferably as described in R. A. Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. ..

    Staining:

    Article Title: Deoxy-cytidine or uridine derivatives for use in cancer therapies
    Article Snippet: .. Microarray Method A comprises the following steps: 1) Extracting RNA from cancer/tumour cells of interest, said extraction preferably being performed using a Norgen Total RNA Purification kit (Norgen Biotek Cat nr. 17200); 2) Preparing Poly(A)+ RNA from the extracted RNA, preferably using a MEGApure kit according to the manufacturer's instructions (Ambion); 3) Preparing complementary DNA (cDNA) from the Poly(A)+ RNA by treatment with reverse transcriptase, i.e. performing reverse transcription; 4) Fragmenting the cDNA using TdT (terminal deoxynucleotidyl transferase); 5) Biotinylating the cDNA fragments using the GeneChip WT Terminal labelling kit (Affymetrix); 6 Repeating steps 1 to 5 with a reference cell line, wherein said reference cell line is MDA-MB-231; 7) Hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 5 to a first DNA microarray at 45° C. for 16 hours, and hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 6, to a DNA microarray at 45° C. for 16 hours, preferably wherein said microarrays are Affymetrix GeneChip Human Gene 2.0 ST Arrays (Applied Biosystems); 8) Washing and staining the hybridized microarrays, preferably in the Affymetrix GeneChip Fluidics Station 450 (Applied Biosystems); 9) Scanning said stained microarrays with the Affymetrix GeneChip Scanner 3000 7G utilising the Affymetrix GeneChip Command Console® software to produce raw data signal values in the form of CEL files; 10) Normalizing the CEL files to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the Affymetrix software package (version 1.36.1), preferably as described in R. A. Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. ..

    Software:

    Article Title: Deoxy-cytidine or uridine derivatives for use in cancer therapies
    Article Snippet: .. Microarray Method A comprises the following steps: 1) Extracting RNA from cancer/tumour cells of interest, said extraction preferably being performed using a Norgen Total RNA Purification kit (Norgen Biotek Cat nr. 17200); 2) Preparing Poly(A)+ RNA from the extracted RNA, preferably using a MEGApure kit according to the manufacturer's instructions (Ambion); 3) Preparing complementary DNA (cDNA) from the Poly(A)+ RNA by treatment with reverse transcriptase, i.e. performing reverse transcription; 4) Fragmenting the cDNA using TdT (terminal deoxynucleotidyl transferase); 5) Biotinylating the cDNA fragments using the GeneChip WT Terminal labelling kit (Affymetrix); 6 Repeating steps 1 to 5 with a reference cell line, wherein said reference cell line is MDA-MB-231; 7) Hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 5 to a first DNA microarray at 45° C. for 16 hours, and hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 6, to a DNA microarray at 45° C. for 16 hours, preferably wherein said microarrays are Affymetrix GeneChip Human Gene 2.0 ST Arrays (Applied Biosystems); 8) Washing and staining the hybridized microarrays, preferably in the Affymetrix GeneChip Fluidics Station 450 (Applied Biosystems); 9) Scanning said stained microarrays with the Affymetrix GeneChip Scanner 3000 7G utilising the Affymetrix GeneChip Command Console® software to produce raw data signal values in the form of CEL files; 10) Normalizing the CEL files to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the Affymetrix software package (version 1.36.1), preferably as described in R. A. Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. ..

    Expressing:

    Article Title: Deoxy-cytidine or uridine derivatives for use in cancer therapies
    Article Snippet: .. Microarray Method A comprises the following steps: 1) Extracting RNA from cancer/tumour cells of interest, said extraction preferably being performed using a Norgen Total RNA Purification kit (Norgen Biotek Cat nr. 17200); 2) Preparing Poly(A)+ RNA from the extracted RNA, preferably using a MEGApure kit according to the manufacturer's instructions (Ambion); 3) Preparing complementary DNA (cDNA) from the Poly(A)+ RNA by treatment with reverse transcriptase, i.e. performing reverse transcription; 4) Fragmenting the cDNA using TdT (terminal deoxynucleotidyl transferase); 5) Biotinylating the cDNA fragments using the GeneChip WT Terminal labelling kit (Affymetrix); 6 Repeating steps 1 to 5 with a reference cell line, wherein said reference cell line is MDA-MB-231; 7) Hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 5 to a first DNA microarray at 45° C. for 16 hours, and hybridizing 5.5 μg of the biotinylated cDNA fragments obtained in step 6, to a DNA microarray at 45° C. for 16 hours, preferably wherein said microarrays are Affymetrix GeneChip Human Gene 2.0 ST Arrays (Applied Biosystems); 8) Washing and staining the hybridized microarrays, preferably in the Affymetrix GeneChip Fluidics Station 450 (Applied Biosystems); 9) Scanning said stained microarrays with the Affymetrix GeneChip Scanner 3000 7G utilising the Affymetrix GeneChip Command Console® software to produce raw data signal values in the form of CEL files; 10) Normalizing the CEL files to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the Affymetrix software package (version 1.36.1), preferably as described in R. A. Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. ..

    Gene Expression:

    Article Title: Identification of lncRNA ZNF252P-AS1 as a novel diagnostic and prognostic biomarker for breast cancer patients: An integrated bioinformatics and experimental analysis.
    Article Snippet: Background: Long non-coding RNAs (lncRNAs) have emerged as useful diagnostic and prognostic markers as well as therapeutic targets in cancer.. Dysregulated levels of lncRNAs have been described in various cancers including breast cancer (BC).. Our study aims to screen novel lncRNAs involved in BC and investigate any possible role in helping diagnosis and determining prognosis of BC patients.



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    Image Search Results


    Top ten upregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

    Journal: Non-Coding RNA

    Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

    doi: 10.3390/ncrna10020025

    Figure Lengend Snippet: Top ten upregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

    Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

    Techniques: Microarray, Software

    Top ten downregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

    Journal: Non-Coding RNA

    Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

    doi: 10.3390/ncrna10020025

    Figure Lengend Snippet: Top ten downregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

    Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

    Techniques: Microarray, Software

    Difference in lncRNA and mRNA fold-changes between the cDNA microarray and in-house RT-qPCR experiments. Data shown are from three independent experiments (in triplicates) with calculated SD values to represent error bars and their statistical analyses were conducted using one-way ANOVA.

    Journal: Non-Coding RNA

    Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

    doi: 10.3390/ncrna10020025

    Figure Lengend Snippet: Difference in lncRNA and mRNA fold-changes between the cDNA microarray and in-house RT-qPCR experiments. Data shown are from three independent experiments (in triplicates) with calculated SD values to represent error bars and their statistical analyses were conducted using one-way ANOVA.

    Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

    Techniques: Microarray, Quantitative RT-PCR

    ( A ) LncRNA-mRNA interaction network was constructed based on the ten selected candidate lncRNAs from the cDNA microarray dataset. The resulting mRNA interactions were predicted using the “rtool” database with −20 kcal as the minimum energy threshold and were filtered to show only mRNAs that were also dysregulated in the dataset. Data were visualized using Cytoscape v3.8.2. (Pink diamond = candidate lncRNA, blue circle = predicted putative mRNA targets). ( B ) A total of nine mRNAs were identified as both responsible in the “regulated exocytosis” hit as well as highly likely to be regulated by the candidate lncRNAs listed in ( A ). Data were visualized using Cytoscape v3.8.2. (pink diamond = candidate regulator lncRNA, blue circle = mRNA predicted involved in the biological process).

    Journal: Non-Coding RNA

    Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

    doi: 10.3390/ncrna10020025

    Figure Lengend Snippet: ( A ) LncRNA-mRNA interaction network was constructed based on the ten selected candidate lncRNAs from the cDNA microarray dataset. The resulting mRNA interactions were predicted using the “rtool” database with −20 kcal as the minimum energy threshold and were filtered to show only mRNAs that were also dysregulated in the dataset. Data were visualized using Cytoscape v3.8.2. (Pink diamond = candidate lncRNA, blue circle = predicted putative mRNA targets). ( B ) A total of nine mRNAs were identified as both responsible in the “regulated exocytosis” hit as well as highly likely to be regulated by the candidate lncRNAs listed in ( A ). Data were visualized using Cytoscape v3.8.2. (pink diamond = candidate regulator lncRNA, blue circle = mRNA predicted involved in the biological process).

    Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

    Techniques: Construct, Microarray

    Comparisons of real-time quantitative reverse transcription PCR, microarrays, and RNA-sequencing and their applications in hepatocellular carcinoma recurrence

    Journal: World Journal of Gastroenterology

    Article Title: Transcriptome analysis creates a new era of precision medicine for managing recurrent hepatocellular carcinoma

    doi: 10.3748/wjg.v29.i5.780

    Figure Lengend Snippet: Comparisons of real-time quantitative reverse transcription PCR, microarrays, and RNA-sequencing and their applications in hepatocellular carcinoma recurrence

    Article Snippet: The surfacing of commercial platforms, such as Human UniGene Set RZPD 1 clone set for cDNA microarrays and Affymetrix Human Genome U95Av2 array for oligonucleotide arrays, have made the technology for both types of arrays widely accessible[ ].

    Techniques: Isolation, cDNA Library Assay, Amplification, Labeling, Fluorescence, Hybridization, Sequencing, High Throughput Screening Assay