other:Article Title: FK506 bypasses the effect of erythroferrone in cancer cachexia skeletal muscle atrophy.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Activin A R&D Cat#338-AC BMP6 Novus Biologicals Cat#6325-BM Cyclosporine A Tocris Biosciences Cat#1101 DMH1 Sigma Cat#D8946 Beta-cyclodextrin Sigma Cat#C4767 Erythroferrone Aviva Systems Biology Cat#OPCA03036 FK506 Cayman Chemical Cat#10007965 Fc hIgG2/FLAG Laboratory of Dr. Léon Kautz N/A Fc-mERFE Laboratory of Dr. Léon Kautz N/A ERFE globular domain (gERFE) Laboratory of Dr. Léon Kautz N/A IL-6 Peprotech Cat#216-16 Puromycin Santa Cruz Biotechnology Cat#sc-108071 Stattic Abcam Cat#120952 Torin-1 Tocris Biosciences Cat#4247 Critical commercial assays Lipofectamine RNAiMAX reagent Thermo Fisher Scientific Cat#13778 Lipofectamine2000 Thermo Fisher Scientific Cat#11668019 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Pierce BCA assay Thermo Fisher Scientific Cat#23225 Mouse ERFE ELISA kit Intrinsic Lifesciences Cat#ERF-200 Protein G-Dynabeads Life technologies Cat10003D QIAquick PCR Purification Kit Qiagen Cat#28104 SYBR GreenER kit Invitrogen Cat#11784200 TRIzol reagent Invitrogen Cat#15596026 High Capacity cDNA Reverse Transcriptase kit Applied Biosystems Cat#4368814 PowerUp SYBR Green master mix Applied Biosystems Cat#A25742 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Endofree Qiagen Plasmid-Giga kit Qiagen Cat#12391 Experimental models: Cell lines C2C12 myoblasts ATCC Cat#CRL-1772; RRID:CVCL_0188 NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK-293T ATCC Cat#CRL-3216 HuH7 Laboratory of Dr. Laura Silvestri N/A C26 Laboratory of Dr. Nicoletta Filigheddu N/A Experimental models: Organisms/strains Female BALB/c Charles River Laboratories N/A Oligonucleotides qPCR SYBR primers See Table S1 for qPCR primers N/A siFkbp12 Qiagen Cat#SI00171052 siAlk2 Qiagen Cat#SI00888874 siAlk3 Qiagen Cat#SI00929971 siCTR Qiagen Cat#1027310 siSTAT3 From Dr. Lidia Avalle GenBank:NM_213659 siCTR (for siSTAT3 experiment) From Dr. Lidia Avalle GenBank:NM_009778 shErfe Eurofins Genomics TRCN0000178969 shFkbp12 Eurofins Genomics TRCN0000012492 shScramble (from siCTR) Eurofins Genomics Cat#1027310 ChIP-qPCR primers See Table S1 for ChIP-qPCR primers N/A (Continued on next page) Cell Reports Medicine 4, 101306, December 19, 2023 e2
Reporter Assay:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
SYBR Green Assay:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Polymerase Chain Reaction:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Reverse Transcription:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Cloning:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Mutagenesis:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Isolation:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Bicinchoninic Acid Protein Assay:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Concentration Assay:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Sequencing:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
RNA sequencing:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Negative Control:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
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