Magnetic Beads:Article Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AID MBL Cat# M214-3; RRID:AB_10897312 EXOSC10 (Figure 1B) abcam Cat# Ab50558; RRID:AB_869937 EXOSC10 (other figures) Santa Cruz Cat# Sc-374595-X; RRID:AB_10990273 DIS3 Bethyl DIS3 Cat# A303-765A; RRID:AB_11205807 Nucleolin abcam Cat# Ab22758; RRID:AB_776878 MTR4 Bethyl Cat# A300-614A; RRID:AB_2187483 GFP abcam Cat# ab290; RRID:AB_303395 EXOSC3 abcam Cat# ab156683; RRID:AB_2619635 MYC Santa Cruz Cat# sc-40; RRID:AB_627268 Mouse Alexa Flour 555 Invitrogen Cat# A-21424; RRID:AB_141780 Rabbit Alexa Fluor 488 Invitrogen Cat# A-11034; RRID:AB_2576217 CPSF73 abcam Cat# ab131245; RRID:AB_11156933 EXOSC2 abcam Cat# ab181211 Tubulin abcam Cat# ab7291; RRID:AB_2241126 Anti-FLAG M2 Magnetic Beads Sigma Cat# M8823-1ML; RRID:AB_2637089 Chemicals, Peptides, and Recombinant Proteins Auxin Sigma Cat# I3750-5G-A Benzonase Sigma Cat# E1014-5KU Critical Commercial Assays Plasmid mini-prep kit QIAGEN Cat# 27106 Gibson assembly mastermix (for cloning) NEB Cat# E5510S GFP-Trap beads Chromotek Cat# Gtma-20 QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat# 200521 QIAquick nucleotide removal kit QIAGEN Cat# 28304 Deposited Data Sequencing data EXOSC10 and DIS3 Gene Expression Omnibus GSE120574 Sequencing data XRN2 Gene Expression Omnibus GSE109003 Uncropped blots Mendeley http://data.mendeley.com/datasets/ jyh2wdyb7z/6 EXOSC10 WT iCLIP Biological replicate 1 & 2 (Macias et al., 2015); Gene Expression Omnibus GSM1892061 & GSM1892062 EXOSC10 CAT iCLIP data Gene Expression Omnibus GSE120574 H3K27ac ChIP-seq Gene Expression Omnibus GSE31755 H3K4me1 ChIP-seq Gene Expression Omnibus GSE31755 H3K4me3 ChIP-seq Gene Expression Omnibus GSE35583 ChIP input control Gene Expression Omnibus GSE31755 Experimental Models: Cell Lines HCT116:TIR1 Eaton et al., 2018 N/A DIS3-AID This paper N/A EXOSC10-AID This paper N/A XRN2-AID Eaton et al., 2018 N/A EXOSC10-AID + EXOSC10 CAT This paper N/A EXOSC10-AID + EXOSC10 WT This paper N/A (Continued on next page) e1 Cell Reports 26, 2779–2791.e1–e5, March 5, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Control siRNA Thermofisher Cat# AM4613 EXOSC10 siRNA Thermofisher Silencer select: S10738 qRT-PCR primers This paper Table S1 iCLIP Oligos König et al., 2010, 2011 Table S2 Northern blot probes This paper Table S2 Recombinant DNA px330 for CRISPR Cong et al., 2013 Addgene Cat# 42230 GFP-MTR4 (Lubas et al., 2011) A kind gift from the lab of Torben Jensen N/A Plasmids for DIS3 tagging This paper Critical sequences in Method Details Plasmids for EXOSC10 tagging This paper Critical sequences in Method Details EXOSC10WT for iCLIP This paper and (Macias et al., 2015) N/A EXOSC10CAT for iCLIP This paper N/A EXOSC10WT for Figure S4A and S4B This paper N/A EXOSC10CAT for Figure S4A and S4B This paper N/A Software and Algorithms pyCRAC Webb et al., 2014 N/A TopHat2 Kim et al., 2013 N/A BEDTools Quinlan and Hall, 2010 N/A ImageJ (colony counting and image processing) N/A MACS2 Zhang et al., 2008 N/A deeptools Ramı́rez et al., 2014 N/A featureCounts Liao et al., 2014 N/A DESeq2 Love et al., 2014 N/A StringTie Pertea et al., 2016 N/A SortMeRNA Kopylova et al., 2012 N/A HISAT2 Kim et al., 2015 N/A SAMTools Li et al., 2009 http://samtools.sourceforge.net/ Other eRNA & PROMPT annotations Chen et al., 2016 N/A
Recombinant:Article Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AID MBL Cat# M214-3; RRID:AB_10897312 EXOSC10 (Figure 1B) abcam Cat# Ab50558; RRID:AB_869937 EXOSC10 (other figures) Santa Cruz Cat# Sc-374595-X; RRID:AB_10990273 DIS3 Bethyl DIS3 Cat# A303-765A; RRID:AB_11205807 Nucleolin abcam Cat# Ab22758; RRID:AB_776878 MTR4 Bethyl Cat# A300-614A; RRID:AB_2187483 GFP abcam Cat# ab290; RRID:AB_303395 EXOSC3 abcam Cat# ab156683; RRID:AB_2619635 MYC Santa Cruz Cat# sc-40; RRID:AB_627268 Mouse Alexa Flour 555 Invitrogen Cat# A-21424; RRID:AB_141780 Rabbit Alexa Fluor 488 Invitrogen Cat# A-11034; RRID:AB_2576217 CPSF73 abcam Cat# ab131245; RRID:AB_11156933 EXOSC2 abcam Cat# ab181211 Tubulin abcam Cat# ab7291; RRID:AB_2241126 Anti-FLAG M2 Magnetic Beads Sigma Cat# M8823-1ML; RRID:AB_2637089 Chemicals, Peptides, and Recombinant Proteins Auxin Sigma Cat# I3750-5G-A Benzonase Sigma Cat# E1014-5KU Critical Commercial Assays Plasmid mini-prep kit QIAGEN Cat# 27106 Gibson assembly mastermix (for cloning) NEB Cat# E5510S GFP-Trap beads Chromotek Cat# Gtma-20 QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat# 200521 QIAquick nucleotide removal kit QIAGEN Cat# 28304 Deposited Data Sequencing data EXOSC10 and DIS3 Gene Expression Omnibus GSE120574 Sequencing data XRN2 Gene Expression Omnibus GSE109003 Uncropped blots Mendeley http://data.mendeley.com/datasets/ jyh2wdyb7z/6 EXOSC10 WT iCLIP Biological replicate 1 & 2 (Macias et al., 2015); Gene Expression Omnibus GSM1892061 & GSM1892062 EXOSC10 CAT iCLIP data Gene Expression Omnibus GSE120574 H3K27ac ChIP-seq Gene Expression Omnibus GSE31755 H3K4me1 ChIP-seq Gene Expression Omnibus GSE31755 H3K4me3 ChIP-seq Gene Expression Omnibus GSE35583 ChIP input control Gene Expression Omnibus GSE31755 Experimental Models: Cell Lines HCT116:TIR1 Eaton et al., 2018 N/A DIS3-AID This paper N/A EXOSC10-AID This paper N/A XRN2-AID Eaton et al., 2018 N/A EXOSC10-AID + EXOSC10 CAT This paper N/A EXOSC10-AID + EXOSC10 WT This paper N/A (Continued on next page) e1 Cell Reports 26, 2779–2791.e1–e5, March 5, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Control siRNA Thermofisher Cat# AM4613 EXOSC10 siRNA Thermofisher Silencer select: S10738 qRT-PCR primers This paper Table S1 iCLIP Oligos König et al., 2010, 2011 Table S2 Northern blot probes This paper Table S2 Recombinant DNA px330 for CRISPR Cong et al., 2013 Addgene Cat# 42230 GFP-MTR4 (Lubas et al., 2011) A kind gift from the lab of Torben Jensen N/A Plasmids for DIS3 tagging This paper Critical sequences in Method Details Plasmids for EXOSC10 tagging This paper Critical sequences in Method Details EXOSC10WT for iCLIP This paper and (Macias et al., 2015) N/A EXOSC10CAT for iCLIP This paper N/A EXOSC10WT for Figure S4A and S4B This paper N/A EXOSC10CAT for Figure S4A and S4B This paper N/A Software and Algorithms pyCRAC Webb et al., 2014 N/A TopHat2 Kim et al., 2013 N/A BEDTools Quinlan and Hall, 2010 N/A ImageJ (colony counting and image processing) N/A MACS2 Zhang et al., 2008 N/A deeptools Ramı́rez et al., 2014 N/A featureCounts Liao et al., 2014 N/A DESeq2 Love et al., 2014 N/A StringTie Pertea et al., 2016 N/A SortMeRNA Kopylova et al., 2012 N/A HISAT2 Kim et al., 2015 N/A SAMTools Li et al., 2009 http://samtools.sourceforge.net/ Other eRNA & PROMPT annotations Chen et al., 2016 N/A
Plasmid Preparation:Article Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AID MBL Cat# M214-3; RRID:AB_10897312 EXOSC10 (Figure 1B) abcam Cat# Ab50558; RRID:AB_869937 EXOSC10 (other figures) Santa Cruz Cat# Sc-374595-X; RRID:AB_10990273 DIS3 Bethyl DIS3 Cat# A303-765A; RRID:AB_11205807 Nucleolin abcam Cat# Ab22758; RRID:AB_776878 MTR4 Bethyl Cat# A300-614A; RRID:AB_2187483 GFP abcam Cat# ab290; RRID:AB_303395 EXOSC3 abcam Cat# ab156683; RRID:AB_2619635 MYC Santa Cruz Cat# sc-40; RRID:AB_627268 Mouse Alexa Flour 555 Invitrogen Cat# A-21424; RRID:AB_141780 Rabbit Alexa Fluor 488 Invitrogen Cat# A-11034; RRID:AB_2576217 CPSF73 abcam Cat# ab131245; RRID:AB_11156933 EXOSC2 abcam Cat# ab181211 Tubulin abcam Cat# ab7291; RRID:AB_2241126 Anti-FLAG M2 Magnetic Beads Sigma Cat# M8823-1ML; RRID:AB_2637089 Chemicals, Peptides, and Recombinant Proteins Auxin Sigma Cat# I3750-5G-A Benzonase Sigma Cat# E1014-5KU Critical Commercial Assays Plasmid mini-prep kit QIAGEN Cat# 27106 Gibson assembly mastermix (for cloning) NEB Cat# E5510S GFP-Trap beads Chromotek Cat# Gtma-20 QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat# 200521 QIAquick nucleotide removal kit QIAGEN Cat# 28304 Deposited Data Sequencing data EXOSC10 and DIS3 Gene Expression Omnibus GSE120574 Sequencing data XRN2 Gene Expression Omnibus GSE109003 Uncropped blots Mendeley http://data.mendeley.com/datasets/ jyh2wdyb7z/6 EXOSC10 WT iCLIP Biological replicate 1 & 2 (Macias et al., 2015); Gene Expression Omnibus GSM1892061 & GSM1892062 EXOSC10 CAT iCLIP data Gene Expression Omnibus GSE120574 H3K27ac ChIP-seq Gene Expression Omnibus GSE31755 H3K4me1 ChIP-seq Gene Expression Omnibus GSE31755 H3K4me3 ChIP-seq Gene Expression Omnibus GSE35583 ChIP input control Gene Expression Omnibus GSE31755 Experimental Models: Cell Lines HCT116:TIR1 Eaton et al., 2018 N/A DIS3-AID This paper N/A EXOSC10-AID This paper N/A XRN2-AID Eaton et al., 2018 N/A EXOSC10-AID + EXOSC10 CAT This paper N/A EXOSC10-AID + EXOSC10 WT This paper N/A (Continued on next page) e1 Cell Reports 26, 2779–2791.e1–e5, March 5, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Control siRNA Thermofisher Cat# AM4613 EXOSC10 siRNA Thermofisher Silencer select: S10738 qRT-PCR primers This paper Table S1 iCLIP Oligos König et al., 2010, 2011 Table S2 Northern blot probes This paper Table S2 Recombinant DNA px330 for CRISPR Cong et al., 2013 Addgene Cat# 42230 GFP-MTR4 (Lubas et al., 2011) A kind gift from the lab of Torben Jensen N/A Plasmids for DIS3 tagging This paper Critical sequences in Method Details Plasmids for EXOSC10 tagging This paper Critical sequences in Method Details EXOSC10WT for iCLIP This paper and (Macias et al., 2015) N/A EXOSC10CAT for iCLIP This paper N/A EXOSC10WT for Figure S4A and S4B This paper N/A EXOSC10CAT for Figure S4A and S4B This paper N/A Software and Algorithms pyCRAC Webb et al., 2014 N/A TopHat2 Kim et al., 2013 N/A BEDTools Quinlan and Hall, 2010 N/A ImageJ (colony counting and image processing) N/A MACS2 Zhang et al., 2008 N/A deeptools Ramı́rez et al., 2014 N/A featureCounts Liao et al., 2014 N/A DESeq2 Love et al., 2014 N/A StringTie Pertea et al., 2016 N/A SortMeRNA Kopylova et al., 2012 N/A HISAT2 Kim et al., 2015 N/A SAMTools Li et al., 2009 http://samtools.sourceforge.net/ Other eRNA & PROMPT annotations Chen et al., 2016 N/A
Cloning:Article Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AID MBL Cat# M214-3; RRID:AB_10897312 EXOSC10 (Figure 1B) abcam Cat# Ab50558; RRID:AB_869937 EXOSC10 (other figures) Santa Cruz Cat# Sc-374595-X; RRID:AB_10990273 DIS3 Bethyl DIS3 Cat# A303-765A; RRID:AB_11205807 Nucleolin abcam Cat# Ab22758; RRID:AB_776878 MTR4 Bethyl Cat# A300-614A; RRID:AB_2187483 GFP abcam Cat# ab290; RRID:AB_303395 EXOSC3 abcam Cat# ab156683; RRID:AB_2619635 MYC Santa Cruz Cat# sc-40; RRID:AB_627268 Mouse Alexa Flour 555 Invitrogen Cat# A-21424; RRID:AB_141780 Rabbit Alexa Fluor 488 Invitrogen Cat# A-11034; RRID:AB_2576217 CPSF73 abcam Cat# ab131245; RRID:AB_11156933 EXOSC2 abcam Cat# ab181211 Tubulin abcam Cat# ab7291; RRID:AB_2241126 Anti-FLAG M2 Magnetic Beads Sigma Cat# M8823-1ML; RRID:AB_2637089 Chemicals, Peptides, and Recombinant Proteins Auxin Sigma Cat# I3750-5G-A Benzonase Sigma Cat# E1014-5KU Critical Commercial Assays Plasmid mini-prep kit QIAGEN Cat# 27106 Gibson assembly mastermix (for cloning) NEB Cat# E5510S GFP-Trap beads Chromotek Cat# Gtma-20 QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat# 200521 QIAquick nucleotide removal kit QIAGEN Cat# 28304 Deposited Data Sequencing data EXOSC10 and DIS3 Gene Expression Omnibus GSE120574 Sequencing data XRN2 Gene Expression Omnibus GSE109003 Uncropped blots Mendeley http://data.mendeley.com/datasets/ jyh2wdyb7z/6 EXOSC10 WT iCLIP Biological replicate 1 & 2 (Macias et al., 2015); Gene Expression Omnibus GSM1892061 & GSM1892062 EXOSC10 CAT iCLIP data Gene Expression Omnibus GSE120574 H3K27ac ChIP-seq Gene Expression Omnibus GSE31755 H3K4me1 ChIP-seq Gene Expression Omnibus GSE31755 H3K4me3 ChIP-seq Gene Expression Omnibus GSE35583 ChIP input control Gene Expression Omnibus GSE31755 Experimental Models: Cell Lines HCT116:TIR1 Eaton et al., 2018 N/A DIS3-AID This paper N/A EXOSC10-AID This paper N/A XRN2-AID Eaton et al., 2018 N/A EXOSC10-AID + EXOSC10 CAT This paper N/A EXOSC10-AID + EXOSC10 WT This paper N/A (Continued on next page) e1 Cell Reports 26, 2779–2791.e1–e5, March 5, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Control siRNA Thermofisher Cat# AM4613 EXOSC10 siRNA Thermofisher Silencer select: S10738 qRT-PCR primers This paper Table S1 iCLIP Oligos König et al., 2010, 2011 Table S2 Northern blot probes This paper Table S2 Recombinant DNA px330 for CRISPR Cong et al., 2013 Addgene Cat# 42230 GFP-MTR4 (Lubas et al., 2011) A kind gift from the lab of Torben Jensen N/A Plasmids for DIS3 tagging This paper Critical sequences in Method Details Plasmids for EXOSC10 tagging This paper Critical sequences in Method Details EXOSC10WT for iCLIP This paper and (Macias et al., 2015) N/A EXOSC10CAT for iCLIP This paper N/A EXOSC10WT for Figure S4A and S4B This paper N/A EXOSC10CAT for Figure S4A and S4B This paper N/A Software and Algorithms pyCRAC Webb et al., 2014 N/A TopHat2 Kim et al., 2013 N/A BEDTools Quinlan and Hall, 2010 N/A ImageJ (colony counting and image processing) N/A MACS2 Zhang et al., 2008 N/A deeptools Ramı́rez et al., 2014 N/A featureCounts Liao et al., 2014 N/A DESeq2 Love et al., 2014 N/A StringTie Pertea et al., 2016 N/A SortMeRNA Kopylova et al., 2012 N/A HISAT2 Kim et al., 2015 N/A SAMTools Li et al., 2009 http://samtools.sourceforge.net/ Other eRNA & PROMPT annotations Chen et al., 2016 N/A
Mutagenesis:Article Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AID MBL Cat# M214-3; RRID:AB_10897312 EXOSC10 (Figure 1B) abcam Cat# Ab50558; RRID:AB_869937 EXOSC10 (other figures) Santa Cruz Cat# Sc-374595-X; RRID:AB_10990273 DIS3 Bethyl DIS3 Cat# A303-765A; RRID:AB_11205807 Nucleolin abcam Cat# Ab22758; RRID:AB_776878 MTR4 Bethyl Cat# A300-614A; RRID:AB_2187483 GFP abcam Cat# ab290; RRID:AB_303395 EXOSC3 abcam Cat# ab156683; RRID:AB_2619635 MYC Santa Cruz Cat# sc-40; RRID:AB_627268 Mouse Alexa Flour 555 Invitrogen Cat# A-21424; RRID:AB_141780 Rabbit Alexa Fluor 488 Invitrogen Cat# A-11034; RRID:AB_2576217 CPSF73 abcam Cat# ab131245; RRID:AB_11156933 EXOSC2 abcam Cat# ab181211 Tubulin abcam Cat# ab7291; RRID:AB_2241126 Anti-FLAG M2 Magnetic Beads Sigma Cat# M8823-1ML; RRID:AB_2637089 Chemicals, Peptides, and Recombinant Proteins Auxin Sigma Cat# I3750-5G-A Benzonase Sigma Cat# E1014-5KU Critical Commercial Assays Plasmid mini-prep kit QIAGEN Cat# 27106 Gibson assembly mastermix (for cloning) NEB Cat# E5510S GFP-Trap beads Chromotek Cat# Gtma-20 QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat# 200521 QIAquick nucleotide removal kit QIAGEN Cat# 28304 Deposited Data Sequencing data EXOSC10 and DIS3 Gene Expression Omnibus GSE120574 Sequencing data XRN2 Gene Expression Omnibus GSE109003 Uncropped blots Mendeley http://data.mendeley.com/datasets/ jyh2wdyb7z/6 EXOSC10 WT iCLIP Biological replicate 1 & 2 (Macias et al., 2015); Gene Expression Omnibus GSM1892061 & GSM1892062 EXOSC10 CAT iCLIP data Gene Expression Omnibus GSE120574 H3K27ac ChIP-seq Gene Expression Omnibus GSE31755 H3K4me1 ChIP-seq Gene Expression Omnibus GSE31755 H3K4me3 ChIP-seq Gene Expression Omnibus GSE35583 ChIP input control Gene Expression Omnibus GSE31755 Experimental Models: Cell Lines HCT116:TIR1 Eaton et al., 2018 N/A DIS3-AID This paper N/A EXOSC10-AID This paper N/A XRN2-AID Eaton et al., 2018 N/A EXOSC10-AID + EXOSC10 CAT This paper N/A EXOSC10-AID + EXOSC10 WT This paper N/A (Continued on next page) e1 Cell Reports 26, 2779–2791.e1–e5, March 5, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Control siRNA Thermofisher Cat# AM4613 EXOSC10 siRNA Thermofisher Silencer select: S10738 qRT-PCR primers This paper Table S1 iCLIP Oligos König et al., 2010, 2011 Table S2 Northern blot probes This paper Table S2 Recombinant DNA px330 for CRISPR Cong et al., 2013 Addgene Cat# 42230 GFP-MTR4 (Lubas et al., 2011) A kind gift from the lab of Torben Jensen N/A Plasmids for DIS3 tagging This paper Critical sequences in Method Details Plasmids for EXOSC10 tagging This paper Critical sequences in Method Details EXOSC10WT for iCLIP This paper and (Macias et al., 2015) N/A EXOSC10CAT for iCLIP This paper N/A EXOSC10WT for Figure S4A and S4B This paper N/A EXOSC10CAT for Figure S4A and S4B This paper N/A Software and Algorithms pyCRAC Webb et al., 2014 N/A TopHat2 Kim et al., 2013 N/A BEDTools Quinlan and Hall, 2010 N/A ImageJ (colony counting and image processing) N/A MACS2 Zhang et al., 2008 N/A deeptools Ramı́rez et al., 2014 N/A featureCounts Liao et al., 2014 N/A DESeq2 Love et al., 2014 N/A StringTie Pertea et al., 2016 N/A SortMeRNA Kopylova et al., 2012 N/A HISAT2 Kim et al., 2015 N/A SAMTools Li et al., 2009 http://samtools.sourceforge.net/ Other eRNA & PROMPT annotations Chen et al., 2016 N/A
Sequencing:Article Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AID MBL Cat# M214-3; RRID:AB_10897312 EXOSC10 (Figure 1B) abcam Cat# Ab50558; RRID:AB_869937 EXOSC10 (other figures) Santa Cruz Cat# Sc-374595-X; RRID:AB_10990273 DIS3 Bethyl DIS3 Cat# A303-765A; RRID:AB_11205807 Nucleolin abcam Cat# Ab22758; RRID:AB_776878 MTR4 Bethyl Cat# A300-614A; RRID:AB_2187483 GFP abcam Cat# ab290; RRID:AB_303395 EXOSC3 abcam Cat# ab156683; RRID:AB_2619635 MYC Santa Cruz Cat# sc-40; RRID:AB_627268 Mouse Alexa Flour 555 Invitrogen Cat# A-21424; RRID:AB_141780 Rabbit Alexa Fluor 488 Invitrogen Cat# A-11034; RRID:AB_2576217 CPSF73 abcam Cat# ab131245; RRID:AB_11156933 EXOSC2 abcam Cat# ab181211 Tubulin abcam Cat# ab7291; RRID:AB_2241126 Anti-FLAG M2 Magnetic Beads Sigma Cat# M8823-1ML; RRID:AB_2637089 Chemicals, Peptides, and Recombinant Proteins Auxin Sigma Cat# I3750-5G-A Benzonase Sigma Cat# E1014-5KU Critical Commercial Assays Plasmid mini-prep kit QIAGEN Cat# 27106 Gibson assembly mastermix (for cloning) NEB Cat# E5510S GFP-Trap beads Chromotek Cat# Gtma-20 QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat# 200521 QIAquick nucleotide removal kit QIAGEN Cat# 28304 Deposited Data Sequencing data EXOSC10 and DIS3 Gene Expression Omnibus GSE120574 Sequencing data XRN2 Gene Expression Omnibus GSE109003 Uncropped blots Mendeley http://data.mendeley.com/datasets/ jyh2wdyb7z/6 EXOSC10 WT iCLIP Biological replicate 1 & 2 (Macias et al., 2015); Gene Expression Omnibus GSM1892061 & GSM1892062 EXOSC10 CAT iCLIP data Gene Expression Omnibus GSE120574 H3K27ac ChIP-seq Gene Expression Omnibus GSE31755 H3K4me1 ChIP-seq Gene Expression Omnibus GSE31755 H3K4me3 ChIP-seq Gene Expression Omnibus GSE35583 ChIP input control Gene Expression Omnibus GSE31755 Experimental Models: Cell Lines HCT116:TIR1 Eaton et al., 2018 N/A DIS3-AID This paper N/A EXOSC10-AID This paper N/A XRN2-AID Eaton et al., 2018 N/A EXOSC10-AID + EXOSC10 CAT This paper N/A EXOSC10-AID + EXOSC10 WT This paper N/A (Continued on next page) e1 Cell Reports 26, 2779–2791.e1–e5, March 5, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Control siRNA Thermofisher Cat# AM4613 EXOSC10 siRNA Thermofisher Silencer select: S10738 qRT-PCR primers This paper Table S1 iCLIP Oligos König et al., 2010, 2011 Table S2 Northern blot probes This paper Table S2 Recombinant DNA px330 for CRISPR Cong et al., 2013 Addgene Cat# 42230 GFP-MTR4 (Lubas et al., 2011) A kind gift from the lab of Torben Jensen N/A Plasmids for DIS3 tagging This paper Critical sequences in Method Details Plasmids for EXOSC10 tagging This paper Critical sequences in Method Details EXOSC10WT for iCLIP This paper and (Macias et al., 2015) N/A EXOSC10CAT for iCLIP This paper N/A EXOSC10WT for Figure S4A and S4B This paper N/A EXOSC10CAT for Figure S4A and S4B This paper N/A Software and Algorithms pyCRAC Webb et al., 2014 N/A TopHat2 Kim et al., 2013 N/A BEDTools Quinlan and Hall, 2010 N/A ImageJ (colony counting and image processing) N/A MACS2 Zhang et al., 2008 N/A deeptools Ramı́rez et al., 2014 N/A featureCounts Liao et al., 2014 N/A DESeq2 Love et al., 2014 N/A StringTie Pertea et al., 2016 N/A SortMeRNA Kopylova et al., 2012 N/A HISAT2 Kim et al., 2015 N/A SAMTools Li et al., 2009 http://samtools.sourceforge.net/ Other eRNA & PROMPT annotations Chen et al., 2016 N/A
Gene Expression:Article Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AID MBL Cat# M214-3; RRID:AB_10897312 EXOSC10 (Figure 1B) abcam Cat# Ab50558; RRID:AB_869937 EXOSC10 (other figures) Santa Cruz Cat# Sc-374595-X; RRID:AB_10990273 DIS3 Bethyl DIS3 Cat# A303-765A; RRID:AB_11205807 Nucleolin abcam Cat# Ab22758; RRID:AB_776878 MTR4 Bethyl Cat# A300-614A; RRID:AB_2187483 GFP abcam Cat# ab290; RRID:AB_303395 EXOSC3 abcam Cat# ab156683; RRID:AB_2619635 MYC Santa Cruz Cat# sc-40; RRID:AB_627268 Mouse Alexa Flour 555 Invitrogen Cat# A-21424; RRID:AB_141780 Rabbit Alexa Fluor 488 Invitrogen Cat# A-11034; RRID:AB_2576217 CPSF73 abcam Cat# ab131245; RRID:AB_11156933 EXOSC2 abcam Cat# ab181211 Tubulin abcam Cat# ab7291; RRID:AB_2241126 Anti-FLAG M2 Magnetic Beads Sigma Cat# M8823-1ML; RRID:AB_2637089 Chemicals, Peptides, and Recombinant Proteins Auxin Sigma Cat# I3750-5G-A Benzonase Sigma Cat# E1014-5KU Critical Commercial Assays Plasmid mini-prep kit QIAGEN Cat# 27106 Gibson assembly mastermix (for cloning) NEB Cat# E5510S GFP-Trap beads Chromotek Cat# Gtma-20 QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat# 200521 QIAquick nucleotide removal kit QIAGEN Cat# 28304 Deposited Data Sequencing data EXOSC10 and DIS3 Gene Expression Omnibus GSE120574 Sequencing data XRN2 Gene Expression Omnibus GSE109003 Uncropped blots Mendeley http://data.mendeley.com/datasets/ jyh2wdyb7z/6 EXOSC10 WT iCLIP Biological replicate 1 & 2 (Macias et al., 2015); Gene Expression Omnibus GSM1892061 & GSM1892062 EXOSC10 CAT iCLIP data Gene Expression Omnibus GSE120574 H3K27ac ChIP-seq Gene Expression Omnibus GSE31755 H3K4me1 ChIP-seq Gene Expression Omnibus GSE31755 H3K4me3 ChIP-seq Gene Expression Omnibus GSE35583 ChIP input control Gene Expression Omnibus GSE31755 Experimental Models: Cell Lines HCT116:TIR1 Eaton et al., 2018 N/A DIS3-AID This paper N/A EXOSC10-AID This paper N/A XRN2-AID Eaton et al., 2018 N/A EXOSC10-AID + EXOSC10 CAT This paper N/A EXOSC10-AID + EXOSC10 WT This paper N/A (Continued on next page) e1 Cell Reports 26, 2779–2791.e1–e5, March 5, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Control siRNA Thermofisher Cat# AM4613 EXOSC10 siRNA Thermofisher Silencer select: S10738 qRT-PCR primers This paper Table S1 iCLIP Oligos König et al., 2010, 2011 Table S2 Northern blot probes This paper Table S2 Recombinant DNA px330 for CRISPR Cong et al., 2013 Addgene Cat# 42230 GFP-MTR4 (Lubas et al., 2011) A kind gift from the lab of Torben Jensen N/A Plasmids for DIS3 tagging This paper Critical sequences in Method Details Plasmids for EXOSC10 tagging This paper Critical sequences in Method Details EXOSC10WT for iCLIP This paper and (Macias et al., 2015) N/A EXOSC10CAT for iCLIP This paper N/A EXOSC10WT for Figure S4A and S4B This paper N/A EXOSC10CAT for Figure S4A and S4B This paper N/A Software and Algorithms pyCRAC Webb et al., 2014 N/A TopHat2 Kim et al., 2013 N/A BEDTools Quinlan and Hall, 2010 N/A ImageJ (colony counting and image processing) N/A MACS2 Zhang et al., 2008 N/A deeptools Ramı́rez et al., 2014 N/A featureCounts Liao et al., 2014 N/A DESeq2 Love et al., 2014 N/A StringTie Pertea et al., 2016 N/A SortMeRNA Kopylova et al., 2012 N/A HISAT2 Kim et al., 2015 N/A SAMTools Li et al., 2009 http://samtools.sourceforge.net/ Other eRNA & PROMPT annotations Chen et al., 2016 N/A
Chromatin Immunoprecipitation:Article Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AID MBL Cat# M214-3; RRID:AB_10897312 EXOSC10 (Figure 1B) abcam Cat# Ab50558; RRID:AB_869937 EXOSC10 (other figures) Santa Cruz Cat# Sc-374595-X; RRID:AB_10990273 DIS3 Bethyl DIS3 Cat# A303-765A; RRID:AB_11205807 Nucleolin abcam Cat# Ab22758; RRID:AB_776878 MTR4 Bethyl Cat# A300-614A; RRID:AB_2187483 GFP abcam Cat# ab290; RRID:AB_303395 EXOSC3 abcam Cat# ab156683; RRID:AB_2619635 MYC Santa Cruz Cat# sc-40; RRID:AB_627268 Mouse Alexa Flour 555 Invitrogen Cat# A-21424; RRID:AB_141780 Rabbit Alexa Fluor 488 Invitrogen Cat# A-11034; RRID:AB_2576217 CPSF73 abcam Cat# ab131245; RRID:AB_11156933 EXOSC2 abcam Cat# ab181211 Tubulin abcam Cat# ab7291; RRID:AB_2241126 Anti-FLAG M2 Magnetic Beads Sigma Cat# M8823-1ML; RRID:AB_2637089 Chemicals, Peptides, and Recombinant Proteins Auxin Sigma Cat# I3750-5G-A Benzonase Sigma Cat# E1014-5KU Critical Commercial Assays Plasmid mini-prep kit QIAGEN Cat# 27106 Gibson assembly mastermix (for cloning) NEB Cat# E5510S GFP-Trap beads Chromotek Cat# Gtma-20 QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat# 200521 QIAquick nucleotide removal kit QIAGEN Cat# 28304 Deposited Data Sequencing data EXOSC10 and DIS3 Gene Expression Omnibus GSE120574 Sequencing data XRN2 Gene Expression Omnibus GSE109003 Uncropped blots Mendeley http://data.mendeley.com/datasets/ jyh2wdyb7z/6 EXOSC10 WT iCLIP Biological replicate 1 & 2 (Macias et al., 2015); Gene Expression Omnibus GSM1892061 & GSM1892062 EXOSC10 CAT iCLIP data Gene Expression Omnibus GSE120574 H3K27ac ChIP-seq Gene Expression Omnibus GSE31755 H3K4me1 ChIP-seq Gene Expression Omnibus GSE31755 H3K4me3 ChIP-seq Gene Expression Omnibus GSE35583 ChIP input control Gene Expression Omnibus GSE31755 Experimental Models: Cell Lines HCT116:TIR1 Eaton et al., 2018 N/A DIS3-AID This paper N/A EXOSC10-AID This paper N/A XRN2-AID Eaton et al., 2018 N/A EXOSC10-AID + EXOSC10 CAT This paper N/A EXOSC10-AID + EXOSC10 WT This paper N/A (Continued on next page) e1 Cell Reports 26, 2779–2791.e1–e5, March 5, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Control siRNA Thermofisher Cat# AM4613 EXOSC10 siRNA Thermofisher Silencer select: S10738 qRT-PCR primers This paper Table S1 iCLIP Oligos König et al., 2010, 2011 Table S2 Northern blot probes This paper Table S2 Recombinant DNA px330 for CRISPR Cong et al., 2013 Addgene Cat# 42230 GFP-MTR4 (Lubas et al., 2011) A kind gift from the lab of Torben Jensen N/A Plasmids for DIS3 tagging This paper Critical sequences in Method Details Plasmids for EXOSC10 tagging This paper Critical sequences in Method Details EXOSC10WT for iCLIP This paper and (Macias et al., 2015) N/A EXOSC10CAT for iCLIP This paper N/A EXOSC10WT for Figure S4A and S4B This paper N/A EXOSC10CAT for Figure S4A and S4B This paper N/A Software and Algorithms pyCRAC Webb et al., 2014 N/A TopHat2 Kim et al., 2013 N/A BEDTools Quinlan and Hall, 2010 N/A ImageJ (colony counting and image processing) N/A MACS2 Zhang et al., 2008 N/A deeptools Ramı́rez et al., 2014 N/A featureCounts Liao et al., 2014 N/A DESeq2 Love et al., 2014 N/A StringTie Pertea et al., 2016 N/A SortMeRNA Kopylova et al., 2012 N/A HISAT2 Kim et al., 2015 N/A SAMTools Li et al., 2009 http://samtools.sourceforge.net/ Other eRNA & PROMPT annotations Chen et al., 2016 N/A
Control:Article Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AID MBL Cat# M214-3; RRID:AB_10897312 EXOSC10 (Figure 1B) abcam Cat# Ab50558; RRID:AB_869937 EXOSC10 (other figures) Santa Cruz Cat# Sc-374595-X; RRID:AB_10990273 DIS3 Bethyl DIS3 Cat# A303-765A; RRID:AB_11205807 Nucleolin abcam Cat# Ab22758; RRID:AB_776878 MTR4 Bethyl Cat# A300-614A; RRID:AB_2187483 GFP abcam Cat# ab290; RRID:AB_303395 EXOSC3 abcam Cat# ab156683; RRID:AB_2619635 MYC Santa Cruz Cat# sc-40; RRID:AB_627268 Mouse Alexa Flour 555 Invitrogen Cat# A-21424; RRID:AB_141780 Rabbit Alexa Fluor 488 Invitrogen Cat# A-11034; RRID:AB_2576217 CPSF73 abcam Cat# ab131245; RRID:AB_11156933 EXOSC2 abcam Cat# ab181211 Tubulin abcam Cat# ab7291; RRID:AB_2241126 Anti-FLAG M2 Magnetic Beads Sigma Cat# M8823-1ML; RRID:AB_2637089 Chemicals, Peptides, and Recombinant Proteins Auxin Sigma Cat# I3750-5G-A Benzonase Sigma Cat# E1014-5KU Critical Commercial Assays Plasmid mini-prep kit QIAGEN Cat# 27106 Gibson assembly mastermix (for cloning) NEB Cat# E5510S GFP-Trap beads Chromotek Cat# Gtma-20 QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat# 200521 QIAquick nucleotide removal kit QIAGEN Cat# 28304 Deposited Data Sequencing data EXOSC10 and DIS3 Gene Expression Omnibus GSE120574 Sequencing data XRN2 Gene Expression Omnibus GSE109003 Uncropped blots Mendeley http://data.mendeley.com/datasets/ jyh2wdyb7z/6 EXOSC10 WT iCLIP Biological replicate 1 & 2 (Macias et al., 2015); Gene Expression Omnibus GSM1892061 & GSM1892062 EXOSC10 CAT iCLIP data Gene Expression Omnibus GSE120574 H3K27ac ChIP-seq Gene Expression Omnibus GSE31755 H3K4me1 ChIP-seq Gene Expression Omnibus GSE31755 H3K4me3 ChIP-seq Gene Expression Omnibus GSE35583 ChIP input control Gene Expression Omnibus GSE31755 Experimental Models: Cell Lines HCT116:TIR1 Eaton et al., 2018 N/A DIS3-AID This paper N/A EXOSC10-AID This paper N/A XRN2-AID Eaton et al., 2018 N/A EXOSC10-AID + EXOSC10 CAT This paper N/A EXOSC10-AID + EXOSC10 WT This paper N/A (Continued on next page) e1 Cell Reports 26, 2779–2791.e1–e5, March 5, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Control siRNA Thermofisher Cat# AM4613 EXOSC10 siRNA Thermofisher Silencer select: S10738 qRT-PCR primers This paper Table S1 iCLIP Oligos König et al., 2010, 2011 Table S2 Northern blot probes This paper Table S2 Recombinant DNA px330 for CRISPR Cong et al., 2013 Addgene Cat# 42230 GFP-MTR4 (Lubas et al., 2011) A kind gift from the lab of Torben Jensen N/A Plasmids for DIS3 tagging This paper Critical sequences in Method Details Plasmids for EXOSC10 tagging This paper Critical sequences in Method Details EXOSC10WT for iCLIP This paper and (Macias et al., 2015) N/A EXOSC10CAT for iCLIP This paper N/A EXOSC10WT for Figure S4A and S4B This paper N/A EXOSC10CAT for Figure S4A and S4B This paper N/A Software and Algorithms pyCRAC Webb et al., 2014 N/A TopHat2 Kim et al., 2013 N/A BEDTools Quinlan and Hall, 2010 N/A ImageJ (colony counting and image processing) N/A MACS2 Zhang et al., 2008 N/A deeptools Ramı́rez et al., 2014 N/A featureCounts Liao et al., 2014 N/A DESeq2 Love et al., 2014 N/A StringTie Pertea et al., 2016 N/A SortMeRNA Kopylova et al., 2012 N/A HISAT2 Kim et al., 2015 N/A SAMTools Li et al., 2009 http://samtools.sourceforge.net/ Other eRNA & PROMPT annotations Chen et al., 2016 N/A
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Bethyl is a verified supplier 
![Fig. 4 | Nuclear retention of US HIV-1 RNA in PBMCs from 22 ART-treated PWH. a PBMCs from healthy donors were left untreated or were treated with PHA [1.66 µg/ml] and after 24 h collected for immunoblotting with the use of anti- MATR3, <t>anti-MTR4,</t> anti-αtubulin and anti-GAPDH antibodies. αtubulin and GAPDH are loading controls. b–e Freshly isolated PBMCs from 16 ART-treated PWH were subjected to nucleocytoplasmic fractionation for subsequent nucleic acid isolation and RT-qPCR quantification of (b) US-short HIV-1 RNA, (c) gapdh mRNA, and (d) US- long HIV-1 RNA. Percentages of each of the measured RNAs in the cytoplasmic fraction are shown in (e). f–k Ex vivo cultures of CD8+-depleted PBMCs from 6 ART- treated PWH were mock-treated, treated with SAHA [0.5 µM], disulfiram [0.5 µM], romidepsin [17.5 nM] or PHA [1.66 µg/ml] as a positive control in the presence of ARV [280 nM ritonavir, 180 nM azidothymidine, 200 nM raltegravir, 100 nM efa- virenz]. Three days post-treatment cells were subjected to nucleocytoplasmic fractionation for subsequent nucleic acid isolation and RT-qPCR quantification of (f, g) US-short HIV-1 RNA, (h, i) gapdh mRNA, and (j, k) US-long HIV-1 RNA. Per- centages of each of the measured RNAs in the cytoplasmic fraction are shown in (g, i, k). b–k Medians are indicated as horizontal lines, and for (e, g, i, k) inter- quartile ranges are indicated as well. The RNA copy numbers were normalized to the cell numbers measured by the beta-actin qPCR assay. Open symbols in (b, d, f, j) indicate undetectable measurements of US RNA that were assigned the values](https://pub-med-unpaywalled-images-cdn.bioz.com/pub_med_ids_ending_with_1667/pm40021667/pm40021667__page8_image1.jpg)