Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Homo sapiens) | HEK293T | Invitrogen | N/A | |
| Cell line (Homo sapiens) | HepG2 | ATCC | RRID:CVCL_0027 | |
| Transfected construct (human) | pcDNA3- Myc-SFPQ | Genscript | This paper | Transfected construct |
| Transfected construct (human) | pcDNA3-Empty Vector | Invitrogen | N/A | Transfected construct |
| Antibody | Anti-SFPQ antibody (Polyclonal, Rabbit) | Abcam | RRID:AB_882523 | WB (1:5,000) |
| Antibody | Anti-nmt55/ p54nrb antibody (Polyclonal, Rabbit) | Abcam | RRID:AB_1269576 | WB (1:20,000) IP (2.5 µg) |
| Antibody | Anti-SFPQ antibody (Monoclonal, Mouse) | Sigma | RRID:AB_260995 | IP (2.5 µg) |
| Antibody | Anti-FLAG antibody (Monoclonal, Mouse) | Sigma | RRID:AB_262044 | IP (2.5 µg) |
| Antibody | Anti-beta Tubulin (Monoclonal, Mouse) | Millipore | RRID:AB_309885 | WB (1:2,000) |
| Antibody | Anti-MYC (Polyclonal, Rabbit) | Sigma | RRID:AB_439694 | WB (1:5,000) |
| Antibody | Anti-Histone H3 antibody (Monoclonal, Rabbit) | Abcam | RRID:AB_302613 | WB (1:1,000) |
| Antibody | Anti-Rabbit antibody (Polyclonal, Goat) | Dako | RRID:AB_2617138 | WB (1:5,000) |
| Antibody | Anti-Mouse antibody (Polyclonal, Goat) | Dako | RRID:AB_2617137 | WB (1:5,000) |
| Sequenced-based reagent | GAPDH FW | This paper | qPCR Primer | GTCAGCCGCATCTTCTTTTG |
| Sequenced-based reagent | GAPDH RE | This paper | qPCR Primer | GCGCCCAATACGACCAAATC |
| Sequenced-based reagent | SFPQ FW | This paper | qPCR Primer | ACAGGGAAAGGCATTGTTGA |
| Sequenced-based reagent | SFPQ RE | This paper | qPCR Primer | TCATCTAGTTGTTCAAGTGGTTCC |
| Sequenced-based reagent | NONO FW | This paper | qPCR Primer | TGATGAAGAGGGACTTCCAGA |
| Sequenced-based reagent | NONO RE | This paper | qPCR Primer | AGCGCATGGCATATTCATACT |
| Sequenced-based reagent | CDYL FW | This paper | qPCR Primer | ACCCACTAGTGCCTCAGGTG |
| Sequenced-based reagent | CDYL lin RE | This paper | qPCR Primer | ATTTCCTTTTGCTGGCAGTC |
| Sequenced-based reagent | CDYL circ RE | This paper | qPCR Primer | CTCGCTGTCATAGCCTTTCC |
| Sequenced-based reagent | ZKSCAN1 FW | This paper | qPCR Primer | CCCAGTCCCACTTCAAACAT |
| Sequenced-based reagent | ZKSCAN1 lin RE | This paper | qPCR Primer | TCCGCTGTGAATAGTGCAGA |
| Sequenced-based reagent | ZKSCAN1 circ RE | This paper | qPCR Primer | TCATTCAGGCTCCAGGAACT |
| Sequenced-based reagent | NEIL3 FW | This paper | qPCR Primer | CAGCCCAATACTCATCACCA |
| Sequenced-based reagent | NEIL3 lin RE | This paper | qPCR Primer | GAGGCGGTTGTGTTTACTGC |
| Sequenced-based reagent | NEIL3 circ RE | This paper | qPCR Primer | CGGGTACTTCATTAAGTGGCTAA |
| Sequenced-based reagent | EYA1 FW | This paper | qPCR Primer | CCAATGCCACTTACCAGCTT |
| Sequenced-based reagent | EYA1 lin RE | This paper | qPCR Primer | TACTGCTCCCAATTGCTGAA |
| Sequenced-based reagent | EYA1 circ RE | This paper | qPCR Primer | TTTCCCATCTGAACCTCGAC |
| Sequenced-based reagent | ARHGAP5 lin FW | This paper | qPCR Primer | CGTGTCAGCGGGAATAAAACT |
| Sequenced-based reagent | ARHGAP5 lin RE | This paper | qPCR Primer | TGGAATTAAAGGATCTGGCAGA |
| Sequenced-based reagent | ARHGAP5 circ Fw | This paper | qPCR Primer | CCTGCAATCACTTCTGACCA |
| Sequenced-based reagent | ARHGAP5 circ RE | This paper | qPCR Primer | TTTGGTTCTTTGTATTTCCCTCA |
| Sequenced-based reagent | DENND1A Upstream FW | This paper | qPCR Primer | CCAAGTTTTGTTTCCCCTTC |
| Sequenced-based reagent | DENND1A Upstream RE | This paper | qPCR Primer | AGAAGCAGCTCTTCGCTCCT |
| Sequenced-based reagent | DENND1A Ex8 FW | This paper | qPCR Primer | ACCAGAGAACTTCCCAGCAT |
| Sequenced-based reagent | DENND1A cSA RE | This paper | qPCR Primer | TGGGAGAGGGGAAATATGTG |
| Sequenced-based reagent | DENND1A Downstream FW | This paper | qPCR Primer | AAGAGCAGCTGCCAAAGACT |
| Sequenced-based reagent | DENND1A Downstream RE | This paper | qPCR Primer | GCGATGTTGCTCTTTGGTCT |
| Sequenced-based reagent | circARHGAP5 intronic Ups Fw | This paper | qPCR Primer | ATGGAATCATTGTGCTTTTC |
| Sequenced-based reagent | circARHGAP5 intronic Ups Re | This paper | qPCR Primer | AATCTTAATCTGGCCCAACTGA |
| Sequenced-based reagent | circARHGAP5 intronic Ds Fw | This paper | qPCR Primer | GGCTAAAAGCTGATTATTTGAAAAG |
| Sequenced-based reagent | circARHGAP5 intronic Ds Re | This paper | qPCR Primer | TACATTTTTCCAGGACTTTGTTCAT |
| Sequenced-based reagent | ARHGAP5 exon five intronic Ups Fw | This paper | qPCR Primer | TGTGGCTAAAACAGGGTGTG |
| Sequenced-based reagent | ARHGAP5 exon five intronic Ups Re | This paper | qPCR Primer | AGGCACCTACAACCAACAGC |
| Sequenced-based reagent | ARHGAP5 exon five intronic Ds Fw | This paper | qPCR Primer | AATGCTGGGTCACTTTGGTC |
| Sequenced-based reagent | ARHGAP5 exon five intronic Ds Re | This paper | qPCR Primer | CAGCCTGGTTCCTAACAAGC |
| Sequenced-based reagent | circCDYL intronic Ups Fw | This paper | qPCR Primer | TTTTGTCTTTGTTTAATGCCATTTC |
| Sequenced-based reagent | circCDYL intronic Ups Re | This paper | qPCR Primer | GGCCAGACTGAGTATACATAAGGAA |
| Sequenced-based reagent | circCDYL intronic Ds Fw | This paper | qPCR Primer | TGACCTGCAAGCTCAGAATGG |
| Sequenced-based reagent | circCDYL intronic Ds Re | This paper | qPCR Primer | GGATTGGTGGTGGAAGTAAAT |
| Sequenced-based reagent | CDYL exon seven intronic Ups Fw | This paper | qPCR Primer | CTGGTTCCTTGTGCCTTGAT |
| Sequenced-based reagent | CDYL exon seven intronic Ups Re | This paper | qPCR Primer | TTTTCAGGGAATGGAACTG |
| Sequenced-based reagent | CDYL exon seven intronic Ds Fw | This paper | qPCR Primer | CCTGCTCCTCACCTTCTCAC |
| Sequenced-based reagent | CDYL exon seven intronic Ds Re |
This paper | qPCR Primer | GTGCTGCTTGTTCCTCTCCT |
| Sequenced-based reagent | circNEIL3 intronic Ups Fw | This paper | qPCR Primer | TTCGAGGCTGCAGTGAACTA |
| Sequenced-based reagent | circNEIL3 intronic Ups Re | This paper | qPCR Primer | TTGCCTTGTTCTTGTCTGGA |
| Sequenced-based reagent | circNEIL3 intronic Ds Fw | This paper | qPCR Primer | CGATCCAAGGTTGGTTGAAT |
| Sequenced-based reagent | circNEIL3 intronic Ds Re | This paper | qPCR Primer | TTTACACCAAATGGTCCCTCA |
| Sequenced-based reagent | NEIL3 exon five intronic Ups Fw |
This paper | qPCR Primer | TACCCAAATCAGTAGGAATGAAGC |
| Sequenced-based reagent | NEIL3 exon five intronic Ups Re | This paper | qPCR Primer | CATACTGAACTCACGTGTTCCAA |
| Sequenced-based reagent | NEIL3 exon five intronic Ds Fw | This paper | qPCR Primer | AACCTGAGGGAGCCAAAGAT |
| Sequenced-based reagent | NEIL3 exon five intronic Ds Re | This paper | qPCR Primer | TGAAGCAGAGACTTTTGAAGG |
| Sequenced-based reagent | circZKSCAN1 intronic Ups Fw | This paper | qPCR Primer | ATGGCCAAGCTGGTCTTGAACTCC |
| Sequenced-based reagent | circZKSCAN1 intronic Ups Re | This paper | qPCR Primer | CAGGAACAGCTGTATGAAATGG |
| Sequenced-based reagent | circZKSCAN1 intronic Ds Fw | This paper | qPCR Primer | TGGAACACTTAACCATGACTGG |
| Sequenced-based reagent | circZKSCAN1 intronic Ds Re | This paper | qPCR Primer | CCATGCCTGGCTGATTTATTAT |
| Sequenced-based reagent | ZKSCAN1 exon four intronic Ups Fw | This paper | qPCR Primer | GCAACAGAGGGAGATGCTG |
| Sequenced-based reagent | ZKSCAN1 exon four intronic Ups Re | This paper | qPCR Primer | GTGTGTGCCAGGATCTTTGA |
| Sequenced-based reagent | ZKSCAN1 exon four intronic Ds Fw | This paper | qPCR Primer | GAAAACTCACAGAATTGGAGAAA |
| Sequenced-based reagent | ZKSCAN1 exon four intronic Ds Re | This paper | qPCR Primer | GGAGCCTTCAGAGGTCACAG |
| Sequenced-based reagent | circEYA1 intronic Ups Fw | This paper | qPCR Primer | CGGTCCATGGTTTTAAGAGTGA |
| Sequenced-based reagent | circEYA1 intronic Ups Re | This paper | qPCR Primer | TGCAACACAAGAAAGGCTGA |
| Sequenced-based reagent | circEYA1 intronic Ds Fw | This paper | qPCR Primer | AGCCTTGTTGTGGAGTAGCT |
| Sequenced-based reagent | circEYA1 intronic Ds Re | This paper | qPCR Primer | TCTTGTTTCCCATGCACACA |
| Sequenced-based reagent | EYA1 exon 12 intronic Ups Fw | This paper | qPCR Primer | CAGATTCTATTTTTGGCATGAGG |
| Sequenced-based reagent | EYA1 exon 12 intronic Ups Re | This paper | qPCR Primer | GGGCAAGTAAACAATTTCCAA |
| Sequenced-based reagent | EYA1 exon 12 intronic Ds Fw | This paper | qPCR Primer | CTCCCATCTCCCACCCTTTC |
| Sequenced-based reagent | EYA1 exon 12 intronic Ds Re | This paper | qPCR Primer | TCTCATCGAGCCTGGTTTGT |
| Sequenced-based reagent | U1 Fw | This paper | qPCR Primer | GCTTATCCATTGCACTCCGG |
| Sequenced-based reagent | U1 Re | This paper | qPCR Primer | CCCCACTACCACAAATTATGCA |
| Sequenced-based reagent | U1 | This paper | Northern blot Probe | ACAAATTATGCAGTCGAGTTTCCCACATTTGGGGAAATCGCAGGGGTCAGCACATCCGGA |
| Sequenced-based reagent | 7SK | This paper | Northern blot Probe | TACTCGTATACCCTTGACCGAAGACCGGTCCTCCTCTATCGGGGATGGTC |
| Sequenced-based reagent | SFPQ siRNA #1 | Merck | SASI_Hs01_00073164 | Sense strand: GUACGAAUAUUCUCAGCGA[dT][dT] Antisense strand: UCGCUGAGAAUAUUCGUAC[dT][dT] |
| Sequenced-based reagent | SFPQ siRNA #2 | Merck | SASI_Hs01_00073165 | Sense strand: GGAAGAUGCCUAUCAUGAA[dT][dT] Antisense strand: UUCAUGAUAGGCAUCUUCC[dT][dT] |
| Sequenced-based reagent | NONO siRNA #1 | Merck | SASI_Hs02_00343478 | Sense strand: GAUGGAAGCUGCACGCCAU[dT][dT] Antisense strand: AUGGCGUGCAGCUUCCAUC[dT][dT] |
| Sequenced-based reagent | NONO siRNA #2 | Merck | SASI_Hs02_00343479 | Sense strand: CUCAGUAUGUGUCCAACGA[dT][dT] Antisense strand: UCGUUGGACACAUACUGAG[dT][dT] |
| Sequenced-based reagent | CTRL siRNA #1 | Merck | CAT#SIC001 | MISSION-siRNA Universal Negative Control #1 |
| Sequenced-based reagent | CTRL siRNA #2 | RiboTask | Targets eGFP Sense strand: GACGUAAACGGCCACAAGUUC Antisense strand: ACUUGUGGCCGUUUACGUCGC |
|
| Commercial assay or kit | DNase I, RNase-free (1 U/µL) | Thermo Fisher Scientific | CAT# EN0521 | DNase Treatment |
| Commercial assay or kit | M-MLV Reverse Transcriptase kit | Thermo Fisher Scientific | CAT# 28025013 | Reverse trancription |
| Commercial assay or kit | NEBNext Poly(A) mRNA Magnetic Isolation Module | New England BioLabs Inc | CAT# E7490S | PolyA RNA selection |
| Commercial assay or kit | RiboCop rRNA Depletion Kit V1.2 | Lexogen | CAT# 037.24 | RNA ribodepletion |
| Commercial assay or kit | SENSE Total RNA-Seq Library Prep Kit | Lexogen | CAT# 009.24 | HEK293T RNA library preparation for total RNA sequencing |
| Commercial assay or kit | QuantSeq 3’ mRNA-Seq Library Prep Kit | Lexogen | CAT# 038.24 |
HEK293T RNA library preparation for 3’end RNA sequencing |
| Chemical compound, drug | Lipofectamine 2000 | Thermo Fisher Scientific | CAT# 12566014 | Transfection HEK293T and HepG2 |
| Chemical compound, drug | Lipofectamine RNAiMAX | Thermo Fisher Scientific | CAT# 13778150 | Transfection HepG2 |
| Chemical compound, drug | SiLentFect Lipid Reagent | Bio-Rad | CAT# 1703361 | Transfection HEK293T |
| Software, algorithm | GraphPad | Prism7 | RRID:SCR_002798 | |
| Software, algorithm | R | R Project for statistical computing | RRID:SCR_001905 | |
| Software, algorithm | Typhoon FLA 9500 | GE Healthcare | V. 1.1.0.187 | Northern blot |
| Software, algorithm | Image Studio | Licor Odyssey Fc | Ver 5.2 | Western blot |
| Software, algorithm | DESeq2, v1.24.0 | Love et al., 2014 | RRID:SCR_015687 | |
| Software, algorithm | STAR, v2.7, | Dobin et al., 2013 | N/A | |
| Software, algorithm | featureCounts, v2.0.0 | Liao et al., 2014 | RRID:SCR_012919 | |
| Software, algorithm | ciri2 | Gao et al., 2015 | N/A | |
| Software, algorithm | find_circ v1.2 | https://github.com/marvin-jens/find_circ | N/A | |
| Software, algorithm | annotate_circ.py | This paper, github/ncrnalab/pyutils | N/A | |
| Software, algorithm | RepeatMasker | UCSC Genome Browser | RRID:SCR_012954 | |
| Software, algorithm | liftOver tool | UCSC genome browser | RRID:SCR_018160 | |
| Software, algorithm | get_flanking spliced_reads.py | This paper, github/ncrnalab/pyutils | N/A | |
| Software, algorithm | get_spliced_reads.py | This paper, github/ncrnalab/pyutils | N/A | |
| Software, algorithm | get_alternative_splicing.py | This paper, github/ncrnalab/pyutils | N/A | |
| Software, algorithm | MACS2 peakcall, v2.2.6 | https://github.com/macs3-project/MACS | RRID:SCR_013291 | |
| Other | Dynabeads Protein A | Thermo Fisher Scientific | CAT# 10001D | RIP |
| Other | Dynabeads Protein G | Thermo Fisher Scientific | CAT# 10003D | RIP |
| Other | TRIzol Reagent | Thermo Fisher Scientific | CAT# 15596018 | RNA Extraction |
| Other | Platinum SYBR Green I Master kit | Thermo Fisher Scientific | CAT# 11733046 | qPCR assay |
| Other | 10% Tris-Glycine SDS-PAGE gel | Thermo Fisher Scientific | CAT# XP00102BOX |
Western blot |
| Other | Immobilon-P Transfer Membrane | EMD Millipore | CAT# IPVH85R |
Western blot |
| Other | SuperSignal West Femto Maximum Sensitivity Substrate kit | Thermo Fisher Scientific | CAT# 34095 | Western blot |
| Other | Amersham Hyperfilm ECL | GE Healthcare | N/A | Western blot |
| Other | Medical film | MG-SR plus, Konica Minolta | N/A | Western blot |