SRX19848661 GSM7138243_r1 SRP430623 PRJNA951665 SRS17207517 GSM7138243 GSM7138243 OTHER TRANSCRIPTOMIC other HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. With three quarters of transfected cells, chromatin RNA was extracted as described in (Sousa-Luís et al 2021 Mol Cel) with the following modifications: chromatin pellet was digested with 2 µl of Turbo DNase (Life Technologies) in 200 µl of High Salt Buffer (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, and 10 mM MgCl2) for 15 min at 37C, then treated with Proteinase K in 0.2% SDS for 10 min at 37C. Chromatin RNA was extracted by phenol/chloroform and a second round of Turbo DNase digestion was performed, followed by RNA extraction using Trizol. ne microgram of chromatin RNA was ribodepleted using RiboCop rRNA Depletion kit (Lexogen), followed by library preparation using NEBNExt Ultra II directional RNA kit. Illumina NovaSeq 6000 SRX19848662 GSM7138244_r1 SRP430623 PRJNA951665 SRS17207514 GSM7138244 GSM7138244 OTHER TRANSCRIPTOMIC other HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. With three quarters of transfected cells, chromatin RNA was extracted as described in (Sousa-Luís et al 2021 Mol Cel) with the following modifications: chromatin pellet was digested with 2 µl of Turbo DNase (Life Technologies) in 200 µl of High Salt Buffer (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, and 10 mM MgCl2) for 15 min at 37C, then treated with Proteinase K in 0.2% SDS for 10 min at 37C. Chromatin RNA was extracted by phenol/chloroform and a second round of Turbo DNase digestion was performed, followed by RNA extraction using Trizol. ne microgram of chromatin RNA was ribodepleted using RiboCop rRNA Depletion kit (Lexogen), followed by library preparation using NEBNExt Ultra II directional RNA kit. Illumina NovaSeq 6000 SRX19848663 GSM7138245_r1 SRP430623 PRJNA951665 SRS17207515 GSM7138245 GSM7138245 OTHER TRANSCRIPTOMIC other HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. With three quarters of transfected cells, chromatin RNA was extracted as described in (Sousa-Luís et al 2021 Mol Cel) with the following modifications: chromatin pellet was digested with 2 µl of Turbo DNase (Life Technologies) in 200 µl of High Salt Buffer (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, and 10 mM MgCl2) for 15 min at 37C, then treated with Proteinase K in 0.2% SDS for 10 min at 37C. Chromatin RNA was extracted by phenol/chloroform and a second round of Turbo DNase digestion was performed, followed by RNA extraction using Trizol. ne microgram of chromatin RNA was ribodepleted using RiboCop rRNA Depletion kit (Lexogen), followed by library preparation using NEBNExt Ultra II directional RNA kit. Illumina NovaSeq 6000 SRX19848664 GSM7138246_r1 SRP430623 PRJNA951665 SRS17207516 GSM7138246 GSM7138246 OTHER TRANSCRIPTOMIC other HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. With three quarters of transfected cells, chromatin RNA was extracted as described in (Sousa-Luís et al 2021 Mol Cel) with the following modifications: chromatin pellet was digested with 2 µl of Turbo DNase (Life Technologies) in 200 µl of High Salt Buffer (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, and 10 mM MgCl2) for 15 min at 37C, then treated with Proteinase K in 0.2% SDS for 10 min at 37C. Chromatin RNA was extracted by phenol/chloroform and a second round of Turbo DNase digestion was performed, followed by RNA extraction using Trizol. ne microgram of chromatin RNA was ribodepleted using RiboCop rRNA Depletion kit (Lexogen), followed by library preparation using NEBNExt Ultra II directional RNA kit. Illumina NovaSeq 6000 SRX19848665 GSM7138247_r1 SRP430623 PRJNA951665 SRS17207520 GSM7138247 GSM7138247 OTHER TRANSCRIPTOMIC other HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. With three quarters of transfected cells, chromatin RNA was extracted as described in (Sousa-Luís et al 2021 Mol Cel) with the following modifications: chromatin pellet was digested with 2 µl of Turbo DNase (Life Technologies) in 200 µl of High Salt Buffer (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, and 10 mM MgCl2) for 15 min at 37C, then treated with Proteinase K in 0.2% SDS for 10 min at 37C. Chromatin RNA was extracted by phenol/chloroform and a second round of Turbo DNase digestion was performed, followed by RNA extraction using Trizol. ne microgram of chromatin RNA was ribodepleted using RiboCop rRNA Depletion kit (Lexogen), followed by library preparation using NEBNExt Ultra II directional RNA kit. Illumina NovaSeq 6000 SRX19848666 GSM7138248_r1 SRP430623 PRJNA951665 SRS17207521 GSM7138248 GSM7138248 OTHER TRANSCRIPTOMIC other HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. With three quarters of transfected cells, chromatin RNA was extracted as described in (Sousa-Luís et al 2021 Mol Cel) with the following modifications: chromatin pellet was digested with 2 µl of Turbo DNase (Life Technologies) in 200 µl of High Salt Buffer (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, and 10 mM MgCl2) for 15 min at 37C, then treated with Proteinase K in 0.2% SDS for 10 min at 37C. Chromatin RNA was extracted by phenol/chloroform and a second round of Turbo DNase digestion was performed, followed by RNA extraction using Trizol. ne microgram of chromatin RNA was ribodepleted using RiboCop rRNA Depletion kit (Lexogen), followed by library preparation using NEBNExt Ultra II directional RNA kit. Illumina NovaSeq 6000 SRX19848667 GSM7138250_r1 SRP430623 PRJNA951665 SRS17207518 GSM7138250 GSM7138250 OTHER TRANSCRIPTOMIC other HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. With three quarters of transfected cells, chromatin RNA was extracted as described in (Sousa-Luís et al 2021 Mol Cel) with the following modifications: chromatin pellet was digested with 2 µl of Turbo DNase (Life Technologies) in 200 µl of High Salt Buffer (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, and 10 mM MgCl2) for 15 min at 37C, then treated with Proteinase K in 0.2% SDS for 10 min at 37C. Chromatin RNA was extracted by phenol/chloroform and a second round of Turbo DNase digestion was performed, followed by RNA extraction using Trizol. ne microgram of chromatin RNA was ribodepleted using RiboCop rRNA Depletion kit (Lexogen), followed by library preparation using NEBNExt Ultra II directional RNA kit. Illumina NovaSeq 6000 SRX19848668 GSM7138251_r1 SRP430623 PRJNA951665 SRS17207519 GSM7138251 GSM7138251 OTHER TRANSCRIPTOMIC other HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. With three quarters of transfected cells, chromatin RNA was extracted as described in (Sousa-Luís et al 2021 Mol Cel) with the following modifications: chromatin pellet was digested with 2 µl of Turbo DNase (Life Technologies) in 200 µl of High Salt Buffer (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, and 10 mM MgCl2) for 15 min at 37C, then treated with Proteinase K in 0.2% SDS for 10 min at 37C. Chromatin RNA was extracted by phenol/chloroform and a second round of Turbo DNase digestion was performed, followed by RNA extraction using Trizol. ne microgram of chromatin RNA was ribodepleted using RiboCop rRNA Depletion kit (Lexogen), followed by library preparation using NEBNExt Ultra II directional RNA kit. Illumina NovaSeq 6000 SRX19848669 GSM7138252_r1 SRP430623 PRJNA951665 SRS17207522 GSM7138252 GSM7138252 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848670 GSM7138253_r1 SRP430623 PRJNA951665 SRS17207525 GSM7138253 GSM7138253 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848671 GSM7138254_r1 SRP430623 PRJNA951665 SRS17207523 GSM7138254 GSM7138254 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848672 GSM7138255_r1 SRP430623 PRJNA951665 SRS17207524 GSM7138255 GSM7138255 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848673 GSM7138257_r1 SRP430623 PRJNA951665 SRS17207527 GSM7138257 GSM7138257 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848674 GSM7138258_r1 SRP430623 PRJNA951665 SRS17207526 GSM7138258 GSM7138258 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848675 GSM7138259_r1 SRP430623 PRJNA951665 SRS17207528 GSM7138259 GSM7138259 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848676 GSM7138260_r1 SRP430623 PRJNA951665 SRS17207529 GSM7138260 GSM7138260 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848677 GSM7138261_r1 SRP430623 PRJNA951665 SRS17207531 GSM7138261 GSM7138261 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848678 GSM7138262_r1 SRP430623 PRJNA951665 SRS17207530 GSM7138262 GSM7138262 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848679 GSM7138264_r1 SRP430623 PRJNA951665 SRS17207532 GSM7138264 GSM7138264 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000 SRX19848680 GSM7138265_r1 SRP430623 PRJNA951665 SRS17207533 GSM7138265 GSM7138265 RNA-Seq TRANSCRIPTOMIC cDNA HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol). Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module. Illumina NovaSeq 6000