Immunofluorescence:Article Title: Milton assembles large mitochondrial clusters, mitoballs, to sustain spermatogenesis
Article Snippet: For PolG1 - Halo flies, the testes were incubated with 0.5 μM HaloTag TMR ligand (1:200, Promega, G8251) for 2 h at room temperature, mounted and imaged as described above. .. The primary antibodies used for immunofluorescence staining include mouse anti-ATP5A (1:1,000, Abcam, ab14748), mouse anti-dsDNA (1:200, Abcam, ab27156), mouse anti-α-spectrin [1:20, Developmental Studies Hybridoma Bank (DSHB), 3A9], and mouse anti-α-tubulin (1:20, DSHB, 12G10). .. The secondary antibodies used include goat anti-mouse IgG Alexa Fluor 488 (1:200, ThermoFisher Scientific, A-11029), goat anti-mouse IgG Alexa Fluor 594 (1:200, ThermoFisher Scientific, A-11005), and goat anti-mouse IgG Alexa Fluor 647 (1:200, ThermoFisher Scientific, A-21235).
Article Title: Milton assembles large mitochondrial clusters, mitoballs, to sustain spermatogenesis.
Article Snippet: For PolG1- Halo flies, the testes were incubated with 0.5 μM HaloTag TMR ligand (1:200, Promega, G8251) for 2 h at room temperature, mounted and imaged as described above. .. The primary antibodies used for immunofluorescence staining include mouse anti- ATP5A (1:1,000, Abcam, ab14748), mouse anti- dsDNA (1:200, Abcam, ab27156), mouse anti- α- spectrin [1:20, Developmental Studies Hybridoma Bank (DSHB), 3A9], and mouse anti- α- tubulin (1:20, DSHB, 12G10). .. The secondary antibodies used include goat anti- mouse IgG Alexa Fluor 488 (1:200, ThermoFisher Scientific, A- 11029), goat anti- mouse IgG Alexa Fluor 594 (1:200, ThermoFisher Scientific, A- 11005), and goat anti- mouse IgG Alexa Fluor 647 (1:200, ThermoFisher Scientific, A- 21235).
Staining:Article Title: Milton assembles large mitochondrial clusters, mitoballs, to sustain spermatogenesis
Article Snippet: For PolG1 - Halo flies, the testes were incubated with 0.5 μM HaloTag TMR ligand (1:200, Promega, G8251) for 2 h at room temperature, mounted and imaged as described above. .. The primary antibodies used for immunofluorescence staining include mouse anti-ATP5A (1:1,000, Abcam, ab14748), mouse anti-dsDNA (1:200, Abcam, ab27156), mouse anti-α-spectrin [1:20, Developmental Studies Hybridoma Bank (DSHB), 3A9], and mouse anti-α-tubulin (1:20, DSHB, 12G10). .. The secondary antibodies used include goat anti-mouse IgG Alexa Fluor 488 (1:200, ThermoFisher Scientific, A-11029), goat anti-mouse IgG Alexa Fluor 594 (1:200, ThermoFisher Scientific, A-11005), and goat anti-mouse IgG Alexa Fluor 647 (1:200, ThermoFisher Scientific, A-21235).
Article Title: Milton assembles large mitochondrial clusters, mitoballs, to sustain spermatogenesis.
Article Snippet: For PolG1- Halo flies, the testes were incubated with 0.5 μM HaloTag TMR ligand (1:200, Promega, G8251) for 2 h at room temperature, mounted and imaged as described above. .. The primary antibodies used for immunofluorescence staining include mouse anti- ATP5A (1:1,000, Abcam, ab14748), mouse anti- dsDNA (1:200, Abcam, ab27156), mouse anti- α- spectrin [1:20, Developmental Studies Hybridoma Bank (DSHB), 3A9], and mouse anti- α- tubulin (1:20, DSHB, 12G10). .. The secondary antibodies used include goat anti- mouse IgG Alexa Fluor 488 (1:200, ThermoFisher Scientific, A- 11029), goat anti- mouse IgG Alexa Fluor 594 (1:200, ThermoFisher Scientific, A- 11005), and goat anti- mouse IgG Alexa Fluor 647 (1:200, ThermoFisher Scientific, A- 21235).
Virus:Article Title: Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-RpL22 This paper N/A Guinea pig anti-RpL22-like This paper N/A Mouse anti-RpL22-like Vassie Ware (Kearse et al.)18 N/A Mouse anti-Fibrillarin [38F3] Abcam Cat#Ab4566; RRID: AB_304523 Guinea pig anti-Vasa Toshie Kai (Patil et al.)80 N/A Mouse anti-a-Spectrin DSHB Cat# 3A9; RRID: AB_528473 Mouse anti-Bam DSHB Cat#Bam; RRID: AB_10570327 Mouse anti-Cyclin B DSHB Cat#F2F4; RRID: AB_528189 Rabbit anti-eIF4E-1 Paul Lasko (Ghosh and Lasko)60 N/A Mouse anti-Lamin Dm0 DSHB Cat#ADL67.10; RRID: AB_528336 Mouse anti-Actin DSHB Cat#JLA20; RRID: AB_528068 Mouse anti-FLAG Sigma Cat#F3165; RRID: AB_259529 Rabbit anti-HA Sigma Cat#H6908; RRID: AB_260070 Bacterial and virus strains Gateway One Shot TOP10 chemically competent E. coli Invitrogen Cat#C404003 Chemicals, peptides, and recombinant proteins TRIzol reagent Invitrogen Cat#15596018 Protein A/G agarose beads Merck Millipore Cat#IP05 cOmplete Protease inhibitor cocktail Roche Cat#11697498001 Critical commercial assays Gateway pENTR/D-TOPO Cloning kit Invitrogen Cat#K240020SP Gateway LR Clonase II Enzyme mix Invitrogen Cat#11791020 Direct-zol miniprep kit Zymo Research Cat#R2052 M-MLV Reverse Transcriptase Promega Cat#M1701 KAPA SYBR FAST qPCR Master Mix ABI Prism Kapa Biosystems Cat#KK4605 Superscript III Reverse Transcriptase Invitrogen Cat#18080-044 BaseScope Assay v2 RED kit ACDbio Cat#323910 Deposited data RNA sequencing data with RNase R treatment This paper PRJNA935838 Experimental models: Cell lines D. melanogaster: S2 (Serum-independent) Steve Cohen N/A D. melanogaster: S2 (Serum-dependent) Chin-Tong Ong N/A Experimental models: Organisms/strains D. melanogaster: Oregon-R-P2 BDSC 2376 D. melanogaster: vasa-Gal4/CyO Yukiko Yamashita (Salzmann et al.)81 N/A D. melanogaster: MTD-Gal4 BDSC 31777 D. melanogaster: RpL22 RNAi [HMS00143] BDSC 34828 D. melanogaster: RpL22 RNAi 2 [KK109432] VDRC 104506 D. melanogaster: RpL22[KG099650/FM7c] BDSC 15203 D. melanogaster: RpL22-like RNAi [GL00729] BDSC 42773 D. melanogaster: smt3 RNAi [HMS01540] BDSC 36125 D. melanogaster: lwr RNAi [GL00624/CyO] BDSC 37481 D. melanogaster: smt3 [04493]/CyO BDSC 11378 (Continued on next page) 16 Cell Reports 43, 114228, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER D. melanogaster: UASp-FLAG-RpL22/TM3 This paper N/A D. melanogaster: UASp-FLAG-RpL22-like/TM3 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #1 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #2 This paper N/A D. melanogaster: circRpL22(NE,3S) CRISPR/FM7c This paper N/A D. melanogaster: hRPL22-HA BDSC 78009 D. melanogaster: hRPL22L1-HA BDSC 78002 Oligonucleotides See Table S1 This paper N/A Recombinant DNA pPFW-RpL22-CDS This paper N/A pPFW-RpL22-like-CDS This paper N/A Valium22-circRpL22-shRNA#1 This paper N/A Valium22-circRpL22-shRNA#2 This paper N/A pAFW-RpL22-CDS This paper N/A pAFW-RpL22-K39R This paper N/A pAFW-RpL22-KNterR This paper N/A Software and algorithms Fiji ImageJ 2.14.0 https://imagej.net/software/fiji/ TopHat 1.4.0 Trapnell et al.82 Bowtie 0.12.9 Langmead et al.83 Other Express Five serum-free medium Gibco Cat#10486-025 Schneider’s Drosophila medium Gibco Cat#21720024 Fetal bovine serum Gibco Cat#10437028 RNase R Epicentre Cat#E0111-20D1 Recombinant RNasin Ribonuclease Inhibitor Promega Cat#N251A Linear Acrylamide Ambion Cat#AM9520 Cellfectin II reagent Gibco Cat#10362100
Recombinant:Article Title: Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-RpL22 This paper N/A Guinea pig anti-RpL22-like This paper N/A Mouse anti-RpL22-like Vassie Ware (Kearse et al.)18 N/A Mouse anti-Fibrillarin [38F3] Abcam Cat#Ab4566; RRID: AB_304523 Guinea pig anti-Vasa Toshie Kai (Patil et al.)80 N/A Mouse anti-a-Spectrin DSHB Cat# 3A9; RRID: AB_528473 Mouse anti-Bam DSHB Cat#Bam; RRID: AB_10570327 Mouse anti-Cyclin B DSHB Cat#F2F4; RRID: AB_528189 Rabbit anti-eIF4E-1 Paul Lasko (Ghosh and Lasko)60 N/A Mouse anti-Lamin Dm0 DSHB Cat#ADL67.10; RRID: AB_528336 Mouse anti-Actin DSHB Cat#JLA20; RRID: AB_528068 Mouse anti-FLAG Sigma Cat#F3165; RRID: AB_259529 Rabbit anti-HA Sigma Cat#H6908; RRID: AB_260070 Bacterial and virus strains Gateway One Shot TOP10 chemically competent E. coli Invitrogen Cat#C404003 Chemicals, peptides, and recombinant proteins TRIzol reagent Invitrogen Cat#15596018 Protein A/G agarose beads Merck Millipore Cat#IP05 cOmplete Protease inhibitor cocktail Roche Cat#11697498001 Critical commercial assays Gateway pENTR/D-TOPO Cloning kit Invitrogen Cat#K240020SP Gateway LR Clonase II Enzyme mix Invitrogen Cat#11791020 Direct-zol miniprep kit Zymo Research Cat#R2052 M-MLV Reverse Transcriptase Promega Cat#M1701 KAPA SYBR FAST qPCR Master Mix ABI Prism Kapa Biosystems Cat#KK4605 Superscript III Reverse Transcriptase Invitrogen Cat#18080-044 BaseScope Assay v2 RED kit ACDbio Cat#323910 Deposited data RNA sequencing data with RNase R treatment This paper PRJNA935838 Experimental models: Cell lines D. melanogaster: S2 (Serum-independent) Steve Cohen N/A D. melanogaster: S2 (Serum-dependent) Chin-Tong Ong N/A Experimental models: Organisms/strains D. melanogaster: Oregon-R-P2 BDSC 2376 D. melanogaster: vasa-Gal4/CyO Yukiko Yamashita (Salzmann et al.)81 N/A D. melanogaster: MTD-Gal4 BDSC 31777 D. melanogaster: RpL22 RNAi [HMS00143] BDSC 34828 D. melanogaster: RpL22 RNAi 2 [KK109432] VDRC 104506 D. melanogaster: RpL22[KG099650/FM7c] BDSC 15203 D. melanogaster: RpL22-like RNAi [GL00729] BDSC 42773 D. melanogaster: smt3 RNAi [HMS01540] BDSC 36125 D. melanogaster: lwr RNAi [GL00624/CyO] BDSC 37481 D. melanogaster: smt3 [04493]/CyO BDSC 11378 (Continued on next page) 16 Cell Reports 43, 114228, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER D. melanogaster: UASp-FLAG-RpL22/TM3 This paper N/A D. melanogaster: UASp-FLAG-RpL22-like/TM3 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #1 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #2 This paper N/A D. melanogaster: circRpL22(NE,3S) CRISPR/FM7c This paper N/A D. melanogaster: hRPL22-HA BDSC 78009 D. melanogaster: hRPL22L1-HA BDSC 78002 Oligonucleotides See Table S1 This paper N/A Recombinant DNA pPFW-RpL22-CDS This paper N/A pPFW-RpL22-like-CDS This paper N/A Valium22-circRpL22-shRNA#1 This paper N/A Valium22-circRpL22-shRNA#2 This paper N/A pAFW-RpL22-CDS This paper N/A pAFW-RpL22-K39R This paper N/A pAFW-RpL22-KNterR This paper N/A Software and algorithms Fiji ImageJ 2.14.0 https://imagej.net/software/fiji/ TopHat 1.4.0 Trapnell et al.82 Bowtie 0.12.9 Langmead et al.83 Other Express Five serum-free medium Gibco Cat#10486-025 Schneider’s Drosophila medium Gibco Cat#21720024 Fetal bovine serum Gibco Cat#10437028 RNase R Epicentre Cat#E0111-20D1 Recombinant RNasin Ribonuclease Inhibitor Promega Cat#N251A Linear Acrylamide Ambion Cat#AM9520 Cellfectin II reagent Gibco Cat#10362100
Protease Inhibitor:Article Title: Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-RpL22 This paper N/A Guinea pig anti-RpL22-like This paper N/A Mouse anti-RpL22-like Vassie Ware (Kearse et al.)18 N/A Mouse anti-Fibrillarin [38F3] Abcam Cat#Ab4566; RRID: AB_304523 Guinea pig anti-Vasa Toshie Kai (Patil et al.)80 N/A Mouse anti-a-Spectrin DSHB Cat# 3A9; RRID: AB_528473 Mouse anti-Bam DSHB Cat#Bam; RRID: AB_10570327 Mouse anti-Cyclin B DSHB Cat#F2F4; RRID: AB_528189 Rabbit anti-eIF4E-1 Paul Lasko (Ghosh and Lasko)60 N/A Mouse anti-Lamin Dm0 DSHB Cat#ADL67.10; RRID: AB_528336 Mouse anti-Actin DSHB Cat#JLA20; RRID: AB_528068 Mouse anti-FLAG Sigma Cat#F3165; RRID: AB_259529 Rabbit anti-HA Sigma Cat#H6908; RRID: AB_260070 Bacterial and virus strains Gateway One Shot TOP10 chemically competent E. coli Invitrogen Cat#C404003 Chemicals, peptides, and recombinant proteins TRIzol reagent Invitrogen Cat#15596018 Protein A/G agarose beads Merck Millipore Cat#IP05 cOmplete Protease inhibitor cocktail Roche Cat#11697498001 Critical commercial assays Gateway pENTR/D-TOPO Cloning kit Invitrogen Cat#K240020SP Gateway LR Clonase II Enzyme mix Invitrogen Cat#11791020 Direct-zol miniprep kit Zymo Research Cat#R2052 M-MLV Reverse Transcriptase Promega Cat#M1701 KAPA SYBR FAST qPCR Master Mix ABI Prism Kapa Biosystems Cat#KK4605 Superscript III Reverse Transcriptase Invitrogen Cat#18080-044 BaseScope Assay v2 RED kit ACDbio Cat#323910 Deposited data RNA sequencing data with RNase R treatment This paper PRJNA935838 Experimental models: Cell lines D. melanogaster: S2 (Serum-independent) Steve Cohen N/A D. melanogaster: S2 (Serum-dependent) Chin-Tong Ong N/A Experimental models: Organisms/strains D. melanogaster: Oregon-R-P2 BDSC 2376 D. melanogaster: vasa-Gal4/CyO Yukiko Yamashita (Salzmann et al.)81 N/A D. melanogaster: MTD-Gal4 BDSC 31777 D. melanogaster: RpL22 RNAi [HMS00143] BDSC 34828 D. melanogaster: RpL22 RNAi 2 [KK109432] VDRC 104506 D. melanogaster: RpL22[KG099650/FM7c] BDSC 15203 D. melanogaster: RpL22-like RNAi [GL00729] BDSC 42773 D. melanogaster: smt3 RNAi [HMS01540] BDSC 36125 D. melanogaster: lwr RNAi [GL00624/CyO] BDSC 37481 D. melanogaster: smt3 [04493]/CyO BDSC 11378 (Continued on next page) 16 Cell Reports 43, 114228, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER D. melanogaster: UASp-FLAG-RpL22/TM3 This paper N/A D. melanogaster: UASp-FLAG-RpL22-like/TM3 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #1 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #2 This paper N/A D. melanogaster: circRpL22(NE,3S) CRISPR/FM7c This paper N/A D. melanogaster: hRPL22-HA BDSC 78009 D. melanogaster: hRPL22L1-HA BDSC 78002 Oligonucleotides See Table S1 This paper N/A Recombinant DNA pPFW-RpL22-CDS This paper N/A pPFW-RpL22-like-CDS This paper N/A Valium22-circRpL22-shRNA#1 This paper N/A Valium22-circRpL22-shRNA#2 This paper N/A pAFW-RpL22-CDS This paper N/A pAFW-RpL22-K39R This paper N/A pAFW-RpL22-KNterR This paper N/A Software and algorithms Fiji ImageJ 2.14.0 https://imagej.net/software/fiji/ TopHat 1.4.0 Trapnell et al.82 Bowtie 0.12.9 Langmead et al.83 Other Express Five serum-free medium Gibco Cat#10486-025 Schneider’s Drosophila medium Gibco Cat#21720024 Fetal bovine serum Gibco Cat#10437028 RNase R Epicentre Cat#E0111-20D1 Recombinant RNasin Ribonuclease Inhibitor Promega Cat#N251A Linear Acrylamide Ambion Cat#AM9520 Cellfectin II reagent Gibco Cat#10362100
Cloning:Article Title: Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-RpL22 This paper N/A Guinea pig anti-RpL22-like This paper N/A Mouse anti-RpL22-like Vassie Ware (Kearse et al.)18 N/A Mouse anti-Fibrillarin [38F3] Abcam Cat#Ab4566; RRID: AB_304523 Guinea pig anti-Vasa Toshie Kai (Patil et al.)80 N/A Mouse anti-a-Spectrin DSHB Cat# 3A9; RRID: AB_528473 Mouse anti-Bam DSHB Cat#Bam; RRID: AB_10570327 Mouse anti-Cyclin B DSHB Cat#F2F4; RRID: AB_528189 Rabbit anti-eIF4E-1 Paul Lasko (Ghosh and Lasko)60 N/A Mouse anti-Lamin Dm0 DSHB Cat#ADL67.10; RRID: AB_528336 Mouse anti-Actin DSHB Cat#JLA20; RRID: AB_528068 Mouse anti-FLAG Sigma Cat#F3165; RRID: AB_259529 Rabbit anti-HA Sigma Cat#H6908; RRID: AB_260070 Bacterial and virus strains Gateway One Shot TOP10 chemically competent E. coli Invitrogen Cat#C404003 Chemicals, peptides, and recombinant proteins TRIzol reagent Invitrogen Cat#15596018 Protein A/G agarose beads Merck Millipore Cat#IP05 cOmplete Protease inhibitor cocktail Roche Cat#11697498001 Critical commercial assays Gateway pENTR/D-TOPO Cloning kit Invitrogen Cat#K240020SP Gateway LR Clonase II Enzyme mix Invitrogen Cat#11791020 Direct-zol miniprep kit Zymo Research Cat#R2052 M-MLV Reverse Transcriptase Promega Cat#M1701 KAPA SYBR FAST qPCR Master Mix ABI Prism Kapa Biosystems Cat#KK4605 Superscript III Reverse Transcriptase Invitrogen Cat#18080-044 BaseScope Assay v2 RED kit ACDbio Cat#323910 Deposited data RNA sequencing data with RNase R treatment This paper PRJNA935838 Experimental models: Cell lines D. melanogaster: S2 (Serum-independent) Steve Cohen N/A D. melanogaster: S2 (Serum-dependent) Chin-Tong Ong N/A Experimental models: Organisms/strains D. melanogaster: Oregon-R-P2 BDSC 2376 D. melanogaster: vasa-Gal4/CyO Yukiko Yamashita (Salzmann et al.)81 N/A D. melanogaster: MTD-Gal4 BDSC 31777 D. melanogaster: RpL22 RNAi [HMS00143] BDSC 34828 D. melanogaster: RpL22 RNAi 2 [KK109432] VDRC 104506 D. melanogaster: RpL22[KG099650/FM7c] BDSC 15203 D. melanogaster: RpL22-like RNAi [GL00729] BDSC 42773 D. melanogaster: smt3 RNAi [HMS01540] BDSC 36125 D. melanogaster: lwr RNAi [GL00624/CyO] BDSC 37481 D. melanogaster: smt3 [04493]/CyO BDSC 11378 (Continued on next page) 16 Cell Reports 43, 114228, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER D. melanogaster: UASp-FLAG-RpL22/TM3 This paper N/A D. melanogaster: UASp-FLAG-RpL22-like/TM3 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #1 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #2 This paper N/A D. melanogaster: circRpL22(NE,3S) CRISPR/FM7c This paper N/A D. melanogaster: hRPL22-HA BDSC 78009 D. melanogaster: hRPL22L1-HA BDSC 78002 Oligonucleotides See Table S1 This paper N/A Recombinant DNA pPFW-RpL22-CDS This paper N/A pPFW-RpL22-like-CDS This paper N/A Valium22-circRpL22-shRNA#1 This paper N/A Valium22-circRpL22-shRNA#2 This paper N/A pAFW-RpL22-CDS This paper N/A pAFW-RpL22-K39R This paper N/A pAFW-RpL22-KNterR This paper N/A Software and algorithms Fiji ImageJ 2.14.0 https://imagej.net/software/fiji/ TopHat 1.4.0 Trapnell et al.82 Bowtie 0.12.9 Langmead et al.83 Other Express Five serum-free medium Gibco Cat#10486-025 Schneider’s Drosophila medium Gibco Cat#21720024 Fetal bovine serum Gibco Cat#10437028 RNase R Epicentre Cat#E0111-20D1 Recombinant RNasin Ribonuclease Inhibitor Promega Cat#N251A Linear Acrylamide Ambion Cat#AM9520 Cellfectin II reagent Gibco Cat#10362100
Reverse Transcription:Article Title: Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-RpL22 This paper N/A Guinea pig anti-RpL22-like This paper N/A Mouse anti-RpL22-like Vassie Ware (Kearse et al.)18 N/A Mouse anti-Fibrillarin [38F3] Abcam Cat#Ab4566; RRID: AB_304523 Guinea pig anti-Vasa Toshie Kai (Patil et al.)80 N/A Mouse anti-a-Spectrin DSHB Cat# 3A9; RRID: AB_528473 Mouse anti-Bam DSHB Cat#Bam; RRID: AB_10570327 Mouse anti-Cyclin B DSHB Cat#F2F4; RRID: AB_528189 Rabbit anti-eIF4E-1 Paul Lasko (Ghosh and Lasko)60 N/A Mouse anti-Lamin Dm0 DSHB Cat#ADL67.10; RRID: AB_528336 Mouse anti-Actin DSHB Cat#JLA20; RRID: AB_528068 Mouse anti-FLAG Sigma Cat#F3165; RRID: AB_259529 Rabbit anti-HA Sigma Cat#H6908; RRID: AB_260070 Bacterial and virus strains Gateway One Shot TOP10 chemically competent E. coli Invitrogen Cat#C404003 Chemicals, peptides, and recombinant proteins TRIzol reagent Invitrogen Cat#15596018 Protein A/G agarose beads Merck Millipore Cat#IP05 cOmplete Protease inhibitor cocktail Roche Cat#11697498001 Critical commercial assays Gateway pENTR/D-TOPO Cloning kit Invitrogen Cat#K240020SP Gateway LR Clonase II Enzyme mix Invitrogen Cat#11791020 Direct-zol miniprep kit Zymo Research Cat#R2052 M-MLV Reverse Transcriptase Promega Cat#M1701 KAPA SYBR FAST qPCR Master Mix ABI Prism Kapa Biosystems Cat#KK4605 Superscript III Reverse Transcriptase Invitrogen Cat#18080-044 BaseScope Assay v2 RED kit ACDbio Cat#323910 Deposited data RNA sequencing data with RNase R treatment This paper PRJNA935838 Experimental models: Cell lines D. melanogaster: S2 (Serum-independent) Steve Cohen N/A D. melanogaster: S2 (Serum-dependent) Chin-Tong Ong N/A Experimental models: Organisms/strains D. melanogaster: Oregon-R-P2 BDSC 2376 D. melanogaster: vasa-Gal4/CyO Yukiko Yamashita (Salzmann et al.)81 N/A D. melanogaster: MTD-Gal4 BDSC 31777 D. melanogaster: RpL22 RNAi [HMS00143] BDSC 34828 D. melanogaster: RpL22 RNAi 2 [KK109432] VDRC 104506 D. melanogaster: RpL22[KG099650/FM7c] BDSC 15203 D. melanogaster: RpL22-like RNAi [GL00729] BDSC 42773 D. melanogaster: smt3 RNAi [HMS01540] BDSC 36125 D. melanogaster: lwr RNAi [GL00624/CyO] BDSC 37481 D. melanogaster: smt3 [04493]/CyO BDSC 11378 (Continued on next page) 16 Cell Reports 43, 114228, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER D. melanogaster: UASp-FLAG-RpL22/TM3 This paper N/A D. melanogaster: UASp-FLAG-RpL22-like/TM3 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #1 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #2 This paper N/A D. melanogaster: circRpL22(NE,3S) CRISPR/FM7c This paper N/A D. melanogaster: hRPL22-HA BDSC 78009 D. melanogaster: hRPL22L1-HA BDSC 78002 Oligonucleotides See Table S1 This paper N/A Recombinant DNA pPFW-RpL22-CDS This paper N/A pPFW-RpL22-like-CDS This paper N/A Valium22-circRpL22-shRNA#1 This paper N/A Valium22-circRpL22-shRNA#2 This paper N/A pAFW-RpL22-CDS This paper N/A pAFW-RpL22-K39R This paper N/A pAFW-RpL22-KNterR This paper N/A Software and algorithms Fiji ImageJ 2.14.0 https://imagej.net/software/fiji/ TopHat 1.4.0 Trapnell et al.82 Bowtie 0.12.9 Langmead et al.83 Other Express Five serum-free medium Gibco Cat#10486-025 Schneider’s Drosophila medium Gibco Cat#21720024 Fetal bovine serum Gibco Cat#10437028 RNase R Epicentre Cat#E0111-20D1 Recombinant RNasin Ribonuclease Inhibitor Promega Cat#N251A Linear Acrylamide Ambion Cat#AM9520 Cellfectin II reagent Gibco Cat#10362100
Real-time Polymerase Chain Reaction:Article Title: Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-RpL22 This paper N/A Guinea pig anti-RpL22-like This paper N/A Mouse anti-RpL22-like Vassie Ware (Kearse et al.)18 N/A Mouse anti-Fibrillarin [38F3] Abcam Cat#Ab4566; RRID: AB_304523 Guinea pig anti-Vasa Toshie Kai (Patil et al.)80 N/A Mouse anti-a-Spectrin DSHB Cat# 3A9; RRID: AB_528473 Mouse anti-Bam DSHB Cat#Bam; RRID: AB_10570327 Mouse anti-Cyclin B DSHB Cat#F2F4; RRID: AB_528189 Rabbit anti-eIF4E-1 Paul Lasko (Ghosh and Lasko)60 N/A Mouse anti-Lamin Dm0 DSHB Cat#ADL67.10; RRID: AB_528336 Mouse anti-Actin DSHB Cat#JLA20; RRID: AB_528068 Mouse anti-FLAG Sigma Cat#F3165; RRID: AB_259529 Rabbit anti-HA Sigma Cat#H6908; RRID: AB_260070 Bacterial and virus strains Gateway One Shot TOP10 chemically competent E. coli Invitrogen Cat#C404003 Chemicals, peptides, and recombinant proteins TRIzol reagent Invitrogen Cat#15596018 Protein A/G agarose beads Merck Millipore Cat#IP05 cOmplete Protease inhibitor cocktail Roche Cat#11697498001 Critical commercial assays Gateway pENTR/D-TOPO Cloning kit Invitrogen Cat#K240020SP Gateway LR Clonase II Enzyme mix Invitrogen Cat#11791020 Direct-zol miniprep kit Zymo Research Cat#R2052 M-MLV Reverse Transcriptase Promega Cat#M1701 KAPA SYBR FAST qPCR Master Mix ABI Prism Kapa Biosystems Cat#KK4605 Superscript III Reverse Transcriptase Invitrogen Cat#18080-044 BaseScope Assay v2 RED kit ACDbio Cat#323910 Deposited data RNA sequencing data with RNase R treatment This paper PRJNA935838 Experimental models: Cell lines D. melanogaster: S2 (Serum-independent) Steve Cohen N/A D. melanogaster: S2 (Serum-dependent) Chin-Tong Ong N/A Experimental models: Organisms/strains D. melanogaster: Oregon-R-P2 BDSC 2376 D. melanogaster: vasa-Gal4/CyO Yukiko Yamashita (Salzmann et al.)81 N/A D. melanogaster: MTD-Gal4 BDSC 31777 D. melanogaster: RpL22 RNAi [HMS00143] BDSC 34828 D. melanogaster: RpL22 RNAi 2 [KK109432] VDRC 104506 D. melanogaster: RpL22[KG099650/FM7c] BDSC 15203 D. melanogaster: RpL22-like RNAi [GL00729] BDSC 42773 D. melanogaster: smt3 RNAi [HMS01540] BDSC 36125 D. melanogaster: lwr RNAi [GL00624/CyO] BDSC 37481 D. melanogaster: smt3 [04493]/CyO BDSC 11378 (Continued on next page) 16 Cell Reports 43, 114228, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER D. melanogaster: UASp-FLAG-RpL22/TM3 This paper N/A D. melanogaster: UASp-FLAG-RpL22-like/TM3 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #1 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #2 This paper N/A D. melanogaster: circRpL22(NE,3S) CRISPR/FM7c This paper N/A D. melanogaster: hRPL22-HA BDSC 78009 D. melanogaster: hRPL22L1-HA BDSC 78002 Oligonucleotides See Table S1 This paper N/A Recombinant DNA pPFW-RpL22-CDS This paper N/A pPFW-RpL22-like-CDS This paper N/A Valium22-circRpL22-shRNA#1 This paper N/A Valium22-circRpL22-shRNA#2 This paper N/A pAFW-RpL22-CDS This paper N/A pAFW-RpL22-K39R This paper N/A pAFW-RpL22-KNterR This paper N/A Software and algorithms Fiji ImageJ 2.14.0 https://imagej.net/software/fiji/ TopHat 1.4.0 Trapnell et al.82 Bowtie 0.12.9 Langmead et al.83 Other Express Five serum-free medium Gibco Cat#10486-025 Schneider’s Drosophila medium Gibco Cat#21720024 Fetal bovine serum Gibco Cat#10437028 RNase R Epicentre Cat#E0111-20D1 Recombinant RNasin Ribonuclease Inhibitor Promega Cat#N251A Linear Acrylamide Ambion Cat#AM9520 Cellfectin II reagent Gibco Cat#10362100
RNA Sequencing:Article Title: Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-RpL22 This paper N/A Guinea pig anti-RpL22-like This paper N/A Mouse anti-RpL22-like Vassie Ware (Kearse et al.)18 N/A Mouse anti-Fibrillarin [38F3] Abcam Cat#Ab4566; RRID: AB_304523 Guinea pig anti-Vasa Toshie Kai (Patil et al.)80 N/A Mouse anti-a-Spectrin DSHB Cat# 3A9; RRID: AB_528473 Mouse anti-Bam DSHB Cat#Bam; RRID: AB_10570327 Mouse anti-Cyclin B DSHB Cat#F2F4; RRID: AB_528189 Rabbit anti-eIF4E-1 Paul Lasko (Ghosh and Lasko)60 N/A Mouse anti-Lamin Dm0 DSHB Cat#ADL67.10; RRID: AB_528336 Mouse anti-Actin DSHB Cat#JLA20; RRID: AB_528068 Mouse anti-FLAG Sigma Cat#F3165; RRID: AB_259529 Rabbit anti-HA Sigma Cat#H6908; RRID: AB_260070 Bacterial and virus strains Gateway One Shot TOP10 chemically competent E. coli Invitrogen Cat#C404003 Chemicals, peptides, and recombinant proteins TRIzol reagent Invitrogen Cat#15596018 Protein A/G agarose beads Merck Millipore Cat#IP05 cOmplete Protease inhibitor cocktail Roche Cat#11697498001 Critical commercial assays Gateway pENTR/D-TOPO Cloning kit Invitrogen Cat#K240020SP Gateway LR Clonase II Enzyme mix Invitrogen Cat#11791020 Direct-zol miniprep kit Zymo Research Cat#R2052 M-MLV Reverse Transcriptase Promega Cat#M1701 KAPA SYBR FAST qPCR Master Mix ABI Prism Kapa Biosystems Cat#KK4605 Superscript III Reverse Transcriptase Invitrogen Cat#18080-044 BaseScope Assay v2 RED kit ACDbio Cat#323910 Deposited data RNA sequencing data with RNase R treatment This paper PRJNA935838 Experimental models: Cell lines D. melanogaster: S2 (Serum-independent) Steve Cohen N/A D. melanogaster: S2 (Serum-dependent) Chin-Tong Ong N/A Experimental models: Organisms/strains D. melanogaster: Oregon-R-P2 BDSC 2376 D. melanogaster: vasa-Gal4/CyO Yukiko Yamashita (Salzmann et al.)81 N/A D. melanogaster: MTD-Gal4 BDSC 31777 D. melanogaster: RpL22 RNAi [HMS00143] BDSC 34828 D. melanogaster: RpL22 RNAi 2 [KK109432] VDRC 104506 D. melanogaster: RpL22[KG099650/FM7c] BDSC 15203 D. melanogaster: RpL22-like RNAi [GL00729] BDSC 42773 D. melanogaster: smt3 RNAi [HMS01540] BDSC 36125 D. melanogaster: lwr RNAi [GL00624/CyO] BDSC 37481 D. melanogaster: smt3 [04493]/CyO BDSC 11378 (Continued on next page) 16 Cell Reports 43, 114228, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER D. melanogaster: UASp-FLAG-RpL22/TM3 This paper N/A D. melanogaster: UASp-FLAG-RpL22-like/TM3 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #1 This paper N/A D. melanogaster: circRpL22(NE,3S) RNAi #2 This paper N/A D. melanogaster: circRpL22(NE,3S) CRISPR/FM7c This paper N/A D. melanogaster: hRPL22-HA BDSC 78009 D. melanogaster: hRPL22L1-HA BDSC 78002 Oligonucleotides See Table S1 This paper N/A Recombinant DNA pPFW-RpL22-CDS This paper N/A pPFW-RpL22-like-CDS This paper N/A Valium22-circRpL22-shRNA#1 This paper N/A Valium22-circRpL22-shRNA#2 This paper N/A pAFW-RpL22-CDS This paper N/A pAFW-RpL22-K39R This paper N/A pAFW-RpL22-KNterR This paper N/A Software and algorithms Fiji ImageJ 2.14.0 https://imagej.net/software/fiji/ TopHat 1.4.0 Trapnell et al.82 Bowtie 0.12.9 Langmead et al.83 Other Express Five serum-free medium Gibco Cat#10486-025 Schneider’s Drosophila medium Gibco Cat#21720024 Fetal bovine serum Gibco Cat#10437028 RNase R Epicentre Cat#E0111-20D1 Recombinant RNasin Ribonuclease Inhibitor Promega Cat#N251A Linear Acrylamide Ambion Cat#AM9520 Cellfectin II reagent Gibco Cat#10362100
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