SRX312111 GSM1171540 SRP026206 PRJNA209070 SRS449707 SAMN02209917 ChIP-Seq GENOMIC ChIP 1. Monoclonal antibodies specific for HA from Sigma Aldrich and the catalog number is 89658 2. Monoclonal antibodies specific for RNAP beta subunit from Neoclone, Madison, WI. The antibody clone was 8RB13 and the catalog number is WP023 3. Monoclonal antibodies specific for RNAP sigma subunit from Neoclone, Madison, WI. The antibody clone was 2G10 and the catalog number is W0004 The cell pellet was resuspended in TE with protease inhibitors. Cells were lysed and DNA was sheered to 100bp fragments in the Covaris focused ultrasonicator. Cell lysates (in 50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing protein-nucleic acid complexes were incubated with immobilized HA specific antibodies to immunoprecipitate CarD containing complexes from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA from the Mc2155 attB::pmsg431. RNAPb and RNAPs containing complexes were immunoprecipitated from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain using specific monoclonal antibodies immobilized on Gammabind sepharose. Co-precipitated complexes were washed 4 times in 10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA with increasing salt. Co-precipitated complexes were eluted in 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% sodium dodecyl sulfate at 65 oC. Eluate crosslinks were reversed by incubating overnight at 65 oC. The samples were treated with 100 ug/ml of proteinase K to each sample and incubate at 37 oC for 2 hours. DNA was extracted by phenol:chloroform:IAA (25:24:1) extraction, precipitated with ethanol, and resuspended in water. AB SOLiD 4 System gds 301171540 GSM1171540 GEO Accession GSM1171540 SRX312112 GSM1171541 SRP026206 PRJNA209070 SRS449708 SAMN02209919 ChIP-Seq GENOMIC ChIP 1. Monoclonal antibodies specific for HA from Sigma Aldrich and the catalog number is 89658 2. Monoclonal antibodies specific for RNAP beta subunit from Neoclone, Madison, WI. The antibody clone was 8RB13 and the catalog number is WP023 3. Monoclonal antibodies specific for RNAP sigma subunit from Neoclone, Madison, WI. The antibody clone was 2G10 and the catalog number is W0004 The cell pellet was resuspended in TE with protease inhibitors. Cells were lysed and DNA was sheered to 100bp fragments in the Covaris focused ultrasonicator. Cell lysates (in 50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing protein-nucleic acid complexes were incubated with immobilized HA specific antibodies to immunoprecipitate CarD containing complexes from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA from the Mc2155 attB::pmsg431. RNAPb and RNAPs containing complexes were immunoprecipitated from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain using specific monoclonal antibodies immobilized on Gammabind sepharose. Co-precipitated complexes were washed 4 times in 10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA with increasing salt. Co-precipitated complexes were eluted in 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% sodium dodecyl sulfate at 65 oC. Eluate crosslinks were reversed by incubating overnight at 65 oC. The samples were treated with 100 ug/ml of proteinase K to each sample and incubate at 37 oC for 2 hours. DNA was extracted by phenol:chloroform:IAA (25:24:1) extraction, precipitated with ethanol, and resuspended in water. AB SOLiD 4 System gds 301171541 GSM1171541 GEO Accession GSM1171541 SRX312113 GSM1171542 SRP026206 PRJNA209070 SRS449709 SAMN02209918 ChIP-Seq GENOMIC ChIP 1. Monoclonal antibodies specific for HA from Sigma Aldrich and the catalog number is 89658 2. Monoclonal antibodies specific for RNAP beta subunit from Neoclone, Madison, WI. The antibody clone was 8RB13 and the catalog number is WP023 3. Monoclonal antibodies specific for RNAP sigma subunit from Neoclone, Madison, WI. The antibody clone was 2G10 and the catalog number is W0004 The cell pellet was resuspended in TE with protease inhibitors. Cells were lysed and DNA was sheered to 100bp fragments in the Covaris focused ultrasonicator. Cell lysates (in 50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing protein-nucleic acid complexes were incubated with immobilized HA specific antibodies to immunoprecipitate CarD containing complexes from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA from the Mc2155 attB::pmsg431. RNAPb and RNAPs containing complexes were immunoprecipitated from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain using specific monoclonal antibodies immobilized on Gammabind sepharose. Co-precipitated complexes were washed 4 times in 10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA with increasing salt. Co-precipitated complexes were eluted in 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% sodium dodecyl sulfate at 65 oC. Eluate crosslinks were reversed by incubating overnight at 65 oC. The samples were treated with 100 ug/ml of proteinase K to each sample and incubate at 37 oC for 2 hours. DNA was extracted by phenol:chloroform:IAA (25:24:1) extraction, precipitated with ethanol, and resuspended in water. AB SOLiD 4 System gds 301171542 GSM1171542 GEO Accession GSM1171542 SRX312114 GSM1171543 SRP026206 PRJNA209070 SRS449710 SAMN02209914 ChIP-Seq GENOMIC ChIP 1. Monoclonal antibodies specific for HA from Sigma Aldrich and the catalog number is 89658 2. Monoclonal antibodies specific for RNAP beta subunit from Neoclone, Madison, WI. The antibody clone was 8RB13 and the catalog number is WP023 3. Monoclonal antibodies specific for RNAP sigma subunit from Neoclone, Madison, WI. The antibody clone was 2G10 and the catalog number is W0004 The cell pellet was resuspended in TE with protease inhibitors. Cells were lysed and DNA was sheered to 100bp fragments in the Covaris focused ultrasonicator. Cell lysates (in 50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing protein-nucleic acid complexes were incubated with immobilized HA specific antibodies to immunoprecipitate CarD containing complexes from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA from the Mc2155 attB::pmsg431. RNAPb and RNAPs containing complexes were immunoprecipitated from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain using specific monoclonal antibodies immobilized on Gammabind sepharose. Co-precipitated complexes were washed 4 times in 10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA with increasing salt. Co-precipitated complexes were eluted in 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% sodium dodecyl sulfate at 65 oC. Eluate crosslinks were reversed by incubating overnight at 65 oC. The samples were treated with 100 ug/ml of proteinase K to each sample and incubate at 37 oC for 2 hours. DNA was extracted by phenol:chloroform:IAA (25:24:1) extraction, precipitated with ethanol, and resuspended in water. AB SOLiD 4 System gds 301171543 GSM1171543 GEO Accession GSM1171543 SRX312115 GSM1171544 SRP026206 PRJNA209070 SRS449711 SAMN02209913 ChIP-Seq GENOMIC ChIP 1. Monoclonal antibodies specific for HA from Sigma Aldrich and the catalog number is 89658 2. Monoclonal antibodies specific for RNAP beta subunit from Neoclone, Madison, WI. The antibody clone was 8RB13 and the catalog number is WP023 3. Monoclonal antibodies specific for RNAP sigma subunit from Neoclone, Madison, WI. The antibody clone was 2G10 and the catalog number is W0004 The cell pellet was resuspended in TE with protease inhibitors. Cells were lysed and DNA was sheered to 100bp fragments in the Covaris focused ultrasonicator. Cell lysates (in 50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing protein-nucleic acid complexes were incubated with immobilized HA specific antibodies to immunoprecipitate CarD containing complexes from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA from the Mc2155 attB::pmsg431. RNAPb and RNAPs containing complexes were immunoprecipitated from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain using specific monoclonal antibodies immobilized on Gammabind sepharose. Co-precipitated complexes were washed 4 times in 10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA with increasing salt. Co-precipitated complexes were eluted in 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% sodium dodecyl sulfate at 65 oC. Eluate crosslinks were reversed by incubating overnight at 65 oC. The samples were treated with 100 ug/ml of proteinase K to each sample and incubate at 37 oC for 2 hours. DNA was extracted by phenol:chloroform:IAA (25:24:1) extraction, precipitated with ethanol, and resuspended in water. AB SOLiD 4 System gds 301171544 GSM1171544 GEO Accession GSM1171544 SRX312116 GSM1171545 SRP026206 PRJNA209070 SRS449712 SAMN02209916 ChIP-Seq GENOMIC ChIP 1. Monoclonal antibodies specific for HA from Sigma Aldrich and the catalog number is 89658 2. Monoclonal antibodies specific for RNAP beta subunit from Neoclone, Madison, WI. The antibody clone was 8RB13 and the catalog number is WP023 3. Monoclonal antibodies specific for RNAP sigma subunit from Neoclone, Madison, WI. The antibody clone was 2G10 and the catalog number is W0004 The cell pellet was resuspended in TE with protease inhibitors. Cells were lysed and DNA was sheered to 100bp fragments in the Covaris focused ultrasonicator. Cell lysates (in 50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing protein-nucleic acid complexes were incubated with immobilized HA specific antibodies to immunoprecipitate CarD containing complexes from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA from the Mc2155 attB::pmsg431. RNAPb and RNAPs containing complexes were immunoprecipitated from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain using specific monoclonal antibodies immobilized on Gammabind sepharose. Co-precipitated complexes were washed 4 times in 10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA with increasing salt. Co-precipitated complexes were eluted in 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% sodium dodecyl sulfate at 65 oC. Eluate crosslinks were reversed by incubating overnight at 65 oC. The samples were treated with 100 ug/ml of proteinase K to each sample and incubate at 37 oC for 2 hours. DNA was extracted by phenol:chloroform:IAA (25:24:1) extraction, precipitated with ethanol, and resuspended in water. AB SOLiD 4 System gds 301171545 GSM1171545 GEO Accession GSM1171545 SRX312117 GSM1171546 SRP026206 PRJNA209070 SRS449713 SAMN02209915 ChIP-Seq GENOMIC ChIP 1. Monoclonal antibodies specific for HA from Sigma Aldrich and the catalog number is 89658 2. Monoclonal antibodies specific for RNAP beta subunit from Neoclone, Madison, WI. The antibody clone was 8RB13 and the catalog number is WP023 3. Monoclonal antibodies specific for RNAP sigma subunit from Neoclone, Madison, WI. The antibody clone was 2G10 and the catalog number is W0004 The cell pellet was resuspended in TE with protease inhibitors. Cells were lysed and DNA was sheered to 100bp fragments in the Covaris focused ultrasonicator. Cell lysates (in 50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing protein-nucleic acid complexes were incubated with immobilized HA specific antibodies to immunoprecipitate CarD containing complexes from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA from the Mc2155 attB::pmsg431. RNAPb and RNAPs containing complexes were immunoprecipitated from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain using specific monoclonal antibodies immobilized on Gammabind sepharose. Co-precipitated complexes were washed 4 times in 10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA with increasing salt. Co-precipitated complexes were eluted in 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% sodium dodecyl sulfate at 65 oC. Eluate crosslinks were reversed by incubating overnight at 65 oC. The samples were treated with 100 ug/ml of proteinase K to each sample and incubate at 37 oC for 2 hours. DNA was extracted by phenol:chloroform:IAA (25:24:1) extraction, precipitated with ethanol, and resuspended in water. AB SOLiD 4 System gds 301171546 GSM1171546 GEO Accession GSM1171546