metadata: run_metadata: 124 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "other" and tissue

124 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "other" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
25182	25182	SRR25670729	SRX21396042	SRS18636200	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA germ ring PAL seq v4	GSM7716871	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA germ ring PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716871	GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER	GSM7716871 r1	GSM7716871	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read2.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read1.fastq.gz	fastq fastq	2834842912.0	9234016.0	GSM7716871 r1	0:52 1:255	A:725811118;C:702410592;G:747583409;T:651018348;N:8019445	52	255	725811118	702410592	747583409	651018348	8019445	SRX21396042	SRS18636200	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00023	0.30494	8e-05	0.01793	0.99967	0.99971	0.5	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25183	25183	SRR25670730	SRX21396042	SRS18636200	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA germ ring PAL seq v4	GSM7716871	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA germ ring PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716871	GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER	GSM7716871 r1	GSM7716871	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3473033898.0	11312814.0	GSM7716871 r2	0:52 1:255	A:853178471;C:899976159;G:962100712;T:750811461;N:6967095	52	255	853178471	899976159	962100712	750811461	6967095	SRX21396042	SRS18636200	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00049	0.0	0.00012	0.0	0.99941	1.0	0.64864		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25184	25184	SRR25670731	SRX21396041	SRS18636199	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA zfs:0000015 PAL seq v4	GSM7716870	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA zfs:0000015 PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716870	GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER	GSM7716870 r1	GSM7716870	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2695203962.0	8779166.0	GSM7716870 r1	0:52 1:255	A:684535386;C:669852151;G:719008886;T:614209811;N:7597728	52	255	684535386	669852151	719008886	614209811	7597728	SRX21396041	SRS18636199	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00117	0.35837	0.00017	0.00682	0.99859	0.99963	0.69473	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25185	25185	SRR25670732	SRX21396041	SRS18636199	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA zfs:0000015 PAL seq v4	GSM7716870	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA zfs:0000015 PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716870	GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER	GSM7716870 r1	GSM7716870	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read2.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read1.fastq.gz	fastq fastq	3476338446.0	11323578.0	GSM7716870 r2	0:52 1:255	A:841832234;C:898325199;G:968774318;T:760398070;N:7008625	52	255	841832234	898325199	968774318	760398070	7008625	SRX21396041	SRS18636199	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00245	0.0	0.00047	0.0	0.99803	1.0	0.58536		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25186	25186	SRR25670733	SRX21396040	SRS18636198	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA sphere PAL seq v4	GSM7716869	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA sphere PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716869	GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER	GSM7716869 r1	GSM7716869	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	3211687254.0	10461522.0	GSM7716869 r1	0:52 1:255	A:813560400;C:775326762;G:854563477;T:759161458;N:9075157	52	255	813560400	775326762	854563477	759161458	9075157	SRX21396040	SRS18636198	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00088	0.43191	0.0004	0.01556	0.99916	0.99961	0.55769	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25187	25187	SRR25670734	SRX21396040	SRS18636198	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA sphere PAL seq v4	GSM7716869	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA sphere PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716869	GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER	GSM7716869 r1	GSM7716869	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3179916131.0	10358033.0	GSM7716869 r2	0:52 1:255	A:771755667;C:804256300;G:883166175;T:714242073;N:6495916	52	255	771755667	804256300	883166175	714242073	6495916	SRX21396040	SRS18636198	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00186	0.0	0.00088	0.0	0.99862	1.0	0.64705		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25188	25188	SRR25670735	SRX21396039	SRS18636197	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA 1024cell PAL seq v4	GSM7716868	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 1024cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716868	GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER	GSM7716868 r1	GSM7716868	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2191900794.0	7139742.0	GSM7716868 r1	0:52 1:255	A:571954354;C:551162617;G:572445400;T:490238669;N:6099754	52	255	571954354	551162617	572445400	490238669	6099754	SRX21396039	SRS18636197	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.0011	0.43387	6e-05	0.01058	0.99864	0.99971	0.74576	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Zygote	Embryo	Embryo Imprecise	All anatomical structures
25189	25189	SRR25670736	SRX21396039	SRS18636197	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA 1024cell PAL seq v4	GSM7716868	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 1024cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716868	GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER	GSM7716868 r1	GSM7716868	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3840723193.0	12510499.0	GSM7716868 r2	0:52 1:255	A:985340216;C:991311706;G:1034487140;T:821820974;N:7763157	52	255	985340216	991311706	1034487140	821820974	7763157	SRX21396039	SRS18636197	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.0021	0.0	0.00026	0.0	0.99859	1.0	0.71022		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Zygote	Embryo	Embryo Imprecise	All anatomical structures
25190	25190	SRR25670737	SRX21396038	SRS18636196	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA 128cell PAL seq v4	GSM7716867	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 128cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716867	GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER	GSM7716867 r1	GSM7716867	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2104868443.0	6856249.0	GSM7716867 r1	0:52 1:255	A:539122676;C:505234642;G:558793048;T:495876292;N:5841785	52	255	539122676	505234642	558793048	495876292	5841785	SRX21396038	SRS18636196	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00035	0.29379	7e-05	0.01129	0.99949	0.99971	0.55882	0.79591	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25191	25191	SRR25670738	SRX21396038	SRS18636196	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA 128cell PAL seq v4	GSM7716867	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 128cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716867	GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER	GSM7716867 r1	GSM7716867	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3135806371.0	10214353.0	GSM7716867 r2	0:52 1:255	A:776612486;C:774126305;G:853951502;T:724788612;N:6327466	52	255	776612486	774126305	853951502	724788612	6327466	SRX21396038	SRS18636196	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00066	0.0	0.00011	0.0	0.99939	1.0	0.55737		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25192	25192	SRR25670739	SRX21396037	SRS18636195	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA 8cell PAL seq v4	GSM7716866	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 8cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716866	GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER	GSM7716866 r1	GSM7716866	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2618998887.0	8530941.0	GSM7716866 r1	0:52 1:255	A:673066508;C:641446717;G:706546263;T:590452494;N:7486905	52	255	673066508	641446717	706546263	590452494	7486905	SRX21396037	SRS18636195	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.0009	0.43244	0.00014	0.0054	0.99902	0.99967	0.54901	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25193	25193	SRR25670740	SRX21396037	SRS18636195	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA 8cell PAL seq v4	GSM7716866	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 8cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716866	GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER	GSM7716866 r1	GSM7716866	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3028839589.0	9865927.0	GSM7716866 r2	0:52 1:255	A:756368817;C:758868409;G:836949742;T:670545278;N:6107343	52	255	756368817	758868409	836949742	670545278	6107343	SRX21396037	SRS18636195	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00156	0.0	0.00026	0.0	0.99835	1.0	0.44791		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25194	25194	SRR25670741	SRX21396036	SRS18636194	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA 1cell PAL seq v4	GSM7716865	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 1cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716865	GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER	GSM7716865 r1	GSM7716865	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_1cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2050143851.0	6677993.0	GSM7716865 r1	0:52 1:255	A:536391564;C:527126186;G:557802929;T:422990166;N:5833006	52	255	536391564	527126186	557802929	422990166	5833006	SRX21396036	SRS18636194	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00016	0.46479	4e-05	0.01408	0.99979	0.99969	0.54545	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Zygote	Embryo	Embryo Imprecise	All anatomical structures
25195	25195	SRR25670742	SRX21396036	SRS18636194	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.		Fish embryo mRNA 1cell PAL seq v4	GSM7716865	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 1cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716865	GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER	GSM7716865 r1	GSM7716865	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680	Fish_embryo_mRNA_1cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3406093776.0	11094768.0	GSM7716865 r2	0:52 1:255	A:868054279;C:890446070;G:945289336;T:695324057;N:6980034	52	255	868054279	890446070	945289336	695324057	6980034	SRX21396036	SRS18636194	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00049	0.0	0.00014	0.0	0.99939	1.0	0.58974		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Zygote	Embryo	Embryo Imprecise	All anatomical structures
33990	33990	SRR31030860	SRX26416598	SRS22936450	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES GAPDH Rep4 minus	GSM8578751	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF NES GAPDH Rep4 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578751	GSM8578751: ZF NES GAPDH Rep4 minus; Danio rerio; OTHER	GSM8578751 r1	GSM8578751	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_GAPDH_Rep4_minus.R1.fq.gz ZF_NES_GAPDH_Rep4_minus.R2.fq.gz	fastq fastq	1100578200.0	3668594.0	GSM8578751 r1	0:150 1:150	A:287878221;C:249390946;G:265835736;T:297454600;N:18697	150	150	287878221	249390946	265835736	297454600	18697	SRX26416598	SRS22936450	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
33991	33991	SRR31030861	SRX26416597	SRS22936451	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES GAPDH Rep3 plus	GSM8578750	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF NES GAPDH Rep3 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578750	GSM8578750: ZF NES GAPDH Rep3 plus; Danio rerio; OTHER	GSM8578750 r1	GSM8578750	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_GAPDH_Rep3_plus.R1.fq.gz ZF_NES_GAPDH_Rep3_plus.R2.fq.gz	fastq fastq	1231779300.0	4105931.0	GSM8578750 r1	0:150 1:150	A:322256597;C:278991471;G:297394980;T:333116282;N:19970	150	150	322256597	278991471	297394980	333116282	19970	SRX26416597	SRS22936451	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
33992	33992	SRR31030862	SRX26416596	SRS22936449	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES GAPDH Rep3 minus	GSM8578749	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF NES GAPDH Rep3 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578749	GSM8578749: ZF NES GAPDH Rep3 minus; Danio rerio; OTHER	GSM8578749 r1	GSM8578749	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_GAPDH_Rep3_minus.R1.fq.gz ZF_NES_GAPDH_Rep3_minus.R2.fq.gz	fastq fastq	1002124500.0	3340415.0	GSM8578749 r1	0:150 1:150	A:262024969;C:227163761;G:242157218;T:270761424;N:17128	150	150	262024969	227163761	242157218	270761424	17128	SRX26416596	SRS22936449	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
33993	33993	SRR31030863	SRX26416595	SRS22936448	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES GAPDH Rep2 plus	GSM8578748	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF NES GAPDH Rep2 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578748	GSM8578748: ZF NES GAPDH Rep2 plus; Danio rerio; OTHER	GSM8578748 r1	GSM8578748	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_GAPDH_Rep2_plus.R1.fq.gz ZF_NES_GAPDH_Rep2_plus.R2.fq.gz	fastq fastq	1051565100.0	3505217.0	GSM8578748 r1	0:150 1:150	A:275784945;C:237523425;G:253300749;T:284937948;N:18033	150	150	275784945	237523425	253300749	284937948	18033	SRX26416595	SRS22936448	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
33994	33994	SRR31030864	SRX26416594	SRS22936447	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES GAPDH Rep2 minus	GSM8578747	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF NES GAPDH Rep2 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578747	GSM8578747: ZF NES GAPDH Rep2 minus; Danio rerio; OTHER	GSM8578747 r1	GSM8578747	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_GAPDH_Rep2_minus.R1.fq.gz ZF_NES_GAPDH_Rep2_minus.R2.fq.gz	fastq fastq	1021837200.0	3406124.0	GSM8578747 r1	0:150 1:150	A:268290250;C:230525208;G:245949056;T:277056045;N:16641	150	150	268290250	230525208	245949056	277056045	16641	SRX26416594	SRS22936447	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
33995	33995	SRR31030865	SRX26416593	SRS22936446	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES GAPDH Rep1 plus	GSM8578746	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF NES GAPDH Rep1 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578746	GSM8578746: ZF NES GAPDH Rep1 plus; Danio rerio; OTHER	GSM8578746 r1	GSM8578746	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_GAPDH_Rep1_plus.R1.fq.gz ZF_NES_GAPDH_Rep1_plus.R2.fq.gz	fastq fastq	1093620300.0	3645401.0	GSM8578746 r1	0:150 1:150	A:285989719;C:247805250;G:264181043;T:295625946;N:18342	150	150	285989719	247805250	264181043	295625946	18342	SRX26416593	SRS22936446	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
33996	33996	SRR31030866	SRX26416592	SRS22936445	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES GAPDH Rep1 minus	GSM8578745	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF NES GAPDH Rep1 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578745	GSM8578745: ZF NES GAPDH Rep1 minus; Danio rerio; OTHER	GSM8578745 r1	GSM8578745	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_GAPDH_Rep1_minus.R1.fq.gz ZF_NES_GAPDH_Rep1_minus.R2.fq.gz	fastq fastq	911747100.0	3039157.0	GSM8578745 r1	0:150 1:150	A:239833349;C:205185786;G:218897710;T:247814511;N:15744	150	150	239833349	205185786	218897710	247814511	15744	SRX26416592	SRS22936445	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
33997	33997	SRR31030867	SRX26416591	SRS22936444	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B MALAT1 Rep4 plus	GSM8578744	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF H2B MALAT1 Rep4 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF	GSM8578744	GSM8578744: ZF H2B MALAT1 Rep4 plus; Danio rerio; OTHER	GSM8578744 r1	GSM8578744	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_MALAT1_Rep4_plus.R1.fq.gz ZF_H2B_MALAT1_Rep4_plus.R2.fq.gz	fastq fastq	842103300.0	2807011.0	GSM8578744 r1	0:150 1:150	A:204870477;C:222752099;G:215404135;T:199062275;N:14314	150	150	204870477	222752099	215404135	199062275	14314	SRX26416591	SRS22936444	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
33998	33998	SRR31030868	SRX26416590	SRS22936442	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B MALAT1 Rep4 minus	GSM8578743	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF H2B MALAT1 Rep4 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF	GSM8578743	GSM8578743: ZF H2B MALAT1 Rep4 minus; Danio rerio; OTHER	GSM8578743 r1	GSM8578743	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_MALAT1_Rep4_minus.R1.fq.gz ZF_H2B_MALAT1_Rep4_minus.R2.fq.gz	fastq fastq	1166375100.0	3887917.0	GSM8578743 r1	0:150 1:150	A:283781955;C:308660466;G:298298204;T:275614377;N:20098	150	150	283781955	308660466	298298204	275614377	20098	SRX26416590	SRS22936442	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
33999	33999	SRR31030869	SRX26416589	SRS22936443	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B MALAT1 Rep3 plus	GSM8578742	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF H2B MALAT1 Rep3 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF	GSM8578742	GSM8578742: ZF H2B MALAT1 Rep3 plus; Danio rerio; OTHER	GSM8578742 r1	GSM8578742	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_MALAT1_Rep3_plus.R1.fq.gz ZF_H2B_MALAT1_Rep3_plus.R2.fq.gz	fastq fastq	1159439400.0	3864798.0	GSM8578742 r1	0:150 1:150	A:282055391;C:306842216;G:296569227;T:273952570;N:19996	150	150	282055391	306842216	296569227	273952570	19996	SRX26416589	SRS22936443	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34000	34000	SRR31030870	SRX26416588	SRS22936440	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B MALAT1 Rep3 minus	GSM8578741	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF H2B MALAT1 Rep3 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF	GSM8578741	GSM8578741: ZF H2B MALAT1 Rep3 minus; Danio rerio; OTHER	GSM8578741 r1	GSM8578741	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_MALAT1_Rep3_minus.R1.fq.gz ZF_H2B_MALAT1_Rep3_minus.R2.fq.gz	fastq fastq	1008297600.0	3360992.0	GSM8578741 r1	0:150 1:150	A:245277585;C:266840408;G:257911846;T:238251305;N:16456	150	150	245277585	266840408	257911846	238251305	16456	SRX26416588	SRS22936440	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34001	34001	SRR31030871	SRX26416587	SRS22936441	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B MALAT1 Rep2 plus	GSM8578740	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF H2B MALAT1 Rep2 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF	GSM8578740	GSM8578740: ZF H2B MALAT1 Rep2 plus; Danio rerio; OTHER	GSM8578740 r1	GSM8578740	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_MALAT1_Rep2_plus.R1.fq.gz ZF_H2B_MALAT1_Rep2_plus.R2.fq.gz	fastq fastq	1419263400.0	4730878.0	GSM8578740 r1	0:150 1:150	A:345302268;C:375591885;G:362956395;T:335387828;N:25024	150	150	345302268	375591885	362956395	335387828	25024	SRX26416587	SRS22936441	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34002	34002	SRR31030872	SRX26416586	SRS22936439	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B MALAT1 Rep2 minus	GSM8578739	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF H2B MALAT1 Rep2 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF	GSM8578739	GSM8578739: ZF H2B MALAT1 Rep2 minus; Danio rerio; OTHER	GSM8578739 r1	GSM8578739	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_MALAT1_Rep2_minus.R1.fq.gz ZF_H2B_MALAT1_Rep2_minus.R2.fq.gz	fastq fastq	1249910700.0	4166369.0	GSM8578739 r1	0:150 1:150	A:304074828;C:330741431;G:319677748;T:295395235;N:21458	150	150	304074828	330741431	319677748	295395235	21458	SRX26416586	SRS22936439	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34003	34003	SRR31030873	SRX26416585	SRS22936438	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B MALAT1 Rep1 plus	GSM8578738	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF H2B MALAT1 Rep1 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF	GSM8578738	GSM8578738: ZF H2B MALAT1 Rep1 plus; Danio rerio; OTHER	GSM8578738 r1	GSM8578738	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_MALAT1_Rep1_plus.R1.fq.gz ZF_H2B_MALAT1_Rep1_plus.R2.fq.gz	fastq fastq	1257872700.0	4192909.0	GSM8578738 r1	0:150 1:150	A:306022947;C:332851039;G:321699513;T:297277788;N:21413	150	150	306022947	332851039	321699513	297277788	21413	SRX26416585	SRS22936438	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34004	34004	SRR31030874	SRX26416584	SRS22936437	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B MALAT1 Rep1 minus	GSM8578737	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF H2B MALAT1 Rep1 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF	GSM8578737	GSM8578737: ZF H2B MALAT1 Rep1 minus; Danio rerio; OTHER	GSM8578737 r1	GSM8578737	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_MALAT1_Rep1_minus.R1.fq.gz ZF_H2B_MALAT1_Rep1_minus.R2.fq.gz	fastq fastq	1377040200.0	4590134.0	GSM8578737 r1	0:150 1:150	A:335021330;C:364359707;G:352178356;T:325457746;N:23061	150	150	335021330	364359707	352178356	325457746	23061	SRX26416584	SRS22936437	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34005	34005	SRR31030875	SRX26416583	SRS22936435	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B GAPDH Rep4 plus	GSM8578736	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF H2B GAPDH Rep4 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF	GSM8578736	GSM8578736: ZF H2B GAPDH Rep4 plus; Danio rerio; OTHER	GSM8578736 r1	GSM8578736	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_GAPDH_Rep4_plus.R1.fq.gz ZF_H2B_GAPDH_Rep4_plus.R2.fq.gz	fastq fastq	1051103100.0	3503677.0	GSM8578736 r1	0:150 1:150	A:274220771;C:238733668;G:254670769;T:283460283;N:17609	150	150	274220771	238733668	254670769	283460283	17609	SRX26416583	SRS22936435	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34006	34006	SRR31030876	SRX26416582	SRS22936436	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B GAPDH Rep4 minus	GSM8578735	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF H2B GAPDH Rep4 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF	GSM8578735	GSM8578735: ZF H2B GAPDH Rep4 minus; Danio rerio; OTHER	GSM8578735 r1	GSM8578735	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_GAPDH_Rep4_minus.R1.fq.gz ZF_H2B_GAPDH_Rep4_minus.R2.fq.gz	fastq fastq	1206485700.0	4021619.0	GSM8578735 r1	0:150 1:150	A:314740194;C:274101014;G:292357972;T:325267132;N:19388	150	150	314740194	274101014	292357972	325267132	19388	SRX26416582	SRS22936436	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34007	34007	SRR31030877	SRX26416581	SRS22936434	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B GAPDH Rep3 plus	GSM8578734	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF H2B GAPDH Rep3 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF	GSM8578734	GSM8578734: ZF H2B GAPDH Rep3 plus; Danio rerio; OTHER	GSM8578734 r1	GSM8578734	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_GAPDH_Rep3_plus.R1.fq.gz ZF_H2B_GAPDH_Rep3_plus.R2.fq.gz	fastq fastq	1140550200.0	3801834.0	GSM8578734 r1	0:150 1:150	A:297636297;C:258828826;G:276373993;T:307692213;N:18871	150	150	297636297	258828826	276373993	307692213	18871	SRX26416581	SRS22936434	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34008	34008	SRR31030878	SRX26416580	SRS22936433	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B GAPDH Rep3 minus	GSM8578733	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF H2B GAPDH Rep3 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF	GSM8578733	GSM8578733: ZF H2B GAPDH Rep3 minus; Danio rerio; OTHER	GSM8578733 r1	GSM8578733	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_GAPDH_Rep3_minus.R1.fq.gz ZF_H2B_GAPDH_Rep3_minus.R2.fq.gz	fastq fastq	782406600.0	2608022.0	GSM8578733 r1	0:150 1:150	A:204132316;C:177696721;G:189675433;T:210888939;N:13191	150	150	204132316	177696721	189675433	210888939	13191	SRX26416580	SRS22936433	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34009	34009	SRR31030879	SRX26416579	SRS22936431	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B GAPDH Rep2 plus	GSM8578732	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF H2B GAPDH Rep2 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF	GSM8578732	GSM8578732: ZF H2B GAPDH Rep2 plus; Danio rerio; OTHER	GSM8578732 r1	GSM8578732	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_GAPDH_Rep2_plus.R1.fq.gz ZF_H2B_GAPDH_Rep2_plus.R2.fq.gz	fastq fastq	958297200.0	3194324.0	GSM8578732 r1	0:150 1:150	A:250011335;C:217600823;G:232206339;T:258462392;N:16311	150	150	250011335	217600823	232206339	258462392	16311	SRX26416579	SRS22936431	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34010	34010	SRR31030880	SRX26416578	SRS22936432	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B GAPDH Rep2 minus	GSM8578731	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF H2B GAPDH Rep2 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF	GSM8578731	GSM8578731: ZF H2B GAPDH Rep2 minus; Danio rerio; OTHER	GSM8578731 r1	GSM8578731	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_GAPDH_Rep2_minus.R1.fq.gz ZF_H2B_GAPDH_Rep2_minus.R2.fq.gz	fastq fastq	1020926700.0	3403089.0	GSM8578731 r1	0:150 1:150	A:266429488;C:231749424;G:247353147;T:275377720;N:16921	150	150	266429488	231749424	247353147	275377720	16921	SRX26416578	SRS22936432	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34011	34011	SRR31030881	SRX26416577	SRS22936430	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B GAPDH Rep1 plus	GSM8578730	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF H2B GAPDH Rep1 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:plus DBF	GSM8578730	GSM8578730: ZF H2B GAPDH Rep1 plus; Danio rerio; OTHER	GSM8578730 r1	GSM8578730	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_GAPDH_Rep1_plus.R1.fq.gz ZF_H2B_GAPDH_Rep1_plus.R2.fq.gz	fastq fastq	1134318600.0	3781062.0	GSM8578730 r1	0:150 1:150	A:295931335;C:257596481;G:274848790;T:305922827;N:19167	150	150	295931335	257596481	274848790	305922827	19167	SRX26416577	SRS22936430	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34012	34012	SRR31030882	SRX26416576	SRS22936429	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF H2B GAPDH Rep1 minus	GSM8578729	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF H2B GAPDH Rep1 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo H2B\|treatment:minus DBF	GSM8578729	GSM8578729: ZF H2B GAPDH Rep1 minus; Danio rerio; OTHER	GSM8578729 r1	GSM8578729	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_H2B_GAPDH_Rep1_minus.R1.fq.gz ZF_H2B_GAPDH_Rep1_minus.R2.fq.gz	fastq fastq	752638800.0	2508796.0	GSM8578729 r1	0:150 1:150	A:196331185;C:170899863;G:182460258;T:202935049;N:12445	150	150	196331185	170899863	182460258	202935049	12445	SRX26416576	SRS22936429	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34013	34013	SRR31031004	SRX26416454	SRS22936307	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb WT pDBF Rep3	GSM8578770	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:wildtype\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	Zeb WT pDBF Rep3	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:wildtype\|treatment:plus DBF	GSM8578770	GSM8578770: Zeb WT pDBF Rep3; Danio rerio; OTHER	GSM8578770 r1	GSM8578770	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_WT_pDBF_Rep3.R1.fq.gz Zeb_WT_pDBF_Rep3.R2.fq.gz	fastq fastq	23216831100.0	77389437.0	GSM8578770 r1	0:150 1:150	A:7577896837;C:3508911439;G:4823311862;T:7306393244;N:317718	150	150	7577896837	3508911439	4823311862	7306393244	317718	SRX26416454	SRS22936307	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34014	34014	SRR31031005	SRX26416453	SRS22936305	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb WT pDBF Rep2	GSM8578769	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:wildtype\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	Zeb WT pDBF Rep2	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:wildtype\|treatment:plus DBF	GSM8578769	GSM8578769: Zeb WT pDBF Rep2; Danio rerio; OTHER	GSM8578769 r1	GSM8578769	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_WT_pDBF_Rep2.R1.fq.gz Zeb_WT_pDBF_Rep2.R2.fq.gz	fastq fastq	27237049500.0	90790165.0	GSM8578769 r1	0:150 1:150	A:8800724632;C:4062692793;G:5651432074;T:8721823175;N:376826	150	150	8800724632	4062692793	5651432074	8721823175	376826	SRX26416453	SRS22936305	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34015	34015	SRR31031006	SRX26416452	SRS22936306	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb WT pDBF Rep1	GSM8578768	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:wildtype\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	Zeb WT pDBF Rep1	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:wildtype\|treatment:plus DBF	GSM8578768	GSM8578768: Zeb WT pDBF Rep1; Danio rerio; OTHER	GSM8578768 r1	GSM8578768	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_WT_pDBF_Rep1.R1.fq.gz Zeb_WT_pDBF_Rep1.R2.fq.gz	fastq fastq	22364115300.0	74547051.0	GSM8578768 r1	0:150 1:150	A:7336106577;C:3346831944;G:4451536371;T:7229335436;N:304972	150	150	7336106577	3346831944	4451536371	7229335436	304972	SRX26416452	SRS22936306	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34016	34016	SRR31031007	SRX26416451	SRS22936304	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb WT mDBF Rep3	GSM8578767	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:wildtype\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	Zeb WT mDBF Rep3	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:wildtype\|treatment:minus DBF	GSM8578767	GSM8578767: Zeb WT mDBF Rep3; Danio rerio; OTHER	GSM8578767 r1	GSM8578767	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_WT_mDBF_Rep3.R1.fq.gz Zeb_WT_mDBF_Rep3.R2.fq.gz	fastq fastq	20112719100.0	67042397.0	GSM8578767 r1	0:150 1:150	A:6537370232;C:2924919118;G:3973928235;T:6676228153;N:273362	150	150	6537370232	2924919118	3973928235	6676228153	273362	SRX26416451	SRS22936304	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34017	34017	SRR31031008	SRX26416450	SRS22936303	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb WT mDBF Rep2	GSM8578766	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:wildtype\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	Zeb WT mDBF Rep2	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:wildtype\|treatment:minus DBF	GSM8578766	GSM8578766: Zeb WT mDBF Rep2; Danio rerio; OTHER	GSM8578766 r1	GSM8578766	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_WT_mDBF_Rep2.R1.fq.gz Zeb_WT_mDBF_Rep2.R2.fq.gz	fastq fastq	24839552100.0	82798507.0	GSM8578766 r1	0:150 1:150	A:8176074473;C:3715794630;G:4984816273;T:7962528150;N:338574	150	150	8176074473	3715794630	4984816273	7962528150	338574	SRX26416450	SRS22936303	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34018	34018	SRR31031009	SRX26416449	SRS22936302	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb WT mDBF Rep1	GSM8578765	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:wildtype\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	Zeb WT mDBF Rep1	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:wildtype\|treatment:minus DBF	GSM8578765	GSM8578765: Zeb WT mDBF Rep1; Danio rerio; OTHER	GSM8578765 r1	GSM8578765	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_WT_mDBF_Rep1.R1.fq.gz Zeb_WT_mDBF_Rep1.R2.fq.gz	fastq fastq	23029785600.0	76765952.0	GSM8578765 r1	0:150 1:150	A:7509388471;C:3438475939;G:4820328116;T:7261277960;N:315114	150	150	7509388471	3438475939	4820328116	7261277960	315114	SRX26416449	SRS22936302	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34019	34019	SRR31031010	SRX26416448	SRS22936301	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb NES pDBF Rep2	GSM8578764	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	Zeb NES pDBF Rep2	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578764	GSM8578764: Zeb NES pDBF Rep2; Danio rerio; OTHER	GSM8578764 r1	GSM8578764	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_NES_pDBF_Rep2.R1.fq.gz Zeb_NES_pDBF_Rep2.R2.fq.gz	fastq fastq	25465584900.0	84885283.0	GSM8578764 r1	0:150 1:150	A:7944190976;C:4330095891;G:5473069331;T:7718120992;N:107710	150	150	7944190976	4330095891	5473069331	7718120992	107710	SRX26416448	SRS22936301	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34020	34020	SRR31031011	SRX26416447	SRS22936300	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb NES pDBF Rep1	GSM8578763	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	Zeb NES pDBF Rep1	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578763	GSM8578763: Zeb NES pDBF Rep1; Danio rerio; OTHER	GSM8578763 r1	GSM8578763	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_NES_pDBF_Rep1.R1.fq.gz Zeb_NES_pDBF_Rep1.R2.fq.gz	fastq fastq	21107351400.0	70357838.0	GSM8578763 r1	0:150 1:150	A:6528579219;C:3620666961;G:4496642830;T:6461373643;N:88747	150	150	6528579219	3620666961	4496642830	6461373643	88747	SRX26416447	SRS22936300	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34021	34021	SRR31031012	SRX26416446	SRS22936299	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb NES mDBF Rep2	GSM8578762	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	Zeb NES mDBF Rep2	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578762	GSM8578762: Zeb NES mDBF Rep2; Danio rerio; OTHER	GSM8578762 r1	GSM8578762	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_NES_mDBF_Rep2.R1.fq.gz Zeb_NES_mDBF_Rep2.R2.fq.gz	fastq fastq	21542967300.0	71809891.0	GSM8578762 r1	0:150 1:150	A:6722613760;C:3654507931;G:4628076548;T:6537678084;N:90977	150	150	6722613760	3654507931	4628076548	6537678084	90977	SRX26416446	SRS22936299	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34022	34022	SRR31031013	SRX26416445	SRS22936297	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	Zeb NES mDBF Rep1	GSM8578761	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	Zeb NES mDBF Rep1	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578761	GSM8578761: Zeb NES mDBF Rep1; Danio rerio; OTHER	GSM8578761 r1	GSM8578761	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	Zeb_NES_mDBF_Rep1.R1.fq.gz Zeb_NES_mDBF_Rep1.R2.fq.gz	fastq fastq	23038870800.0	76796236.0	GSM8578761 r1	0:150 1:150	A:7216059153;C:3815899397;G:4909028200;T:7097787584;N:96466	150	150	7216059153	3815899397	4909028200	7097787584	96466	SRX26416445	SRS22936297	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34023	34023	SRR31031014	SRX26416444	SRS22936298	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES MALAT1 Rep4 plus	GSM8578760	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF NES MALAT1 Rep4 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578760	GSM8578760: ZF NES MALAT1 Rep4 plus; Danio rerio; OTHER	GSM8578760 r1	GSM8578760	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_MALAT1_Rep4_plus.R1.fq.gz ZF_NES_MALAT1_Rep4_plus.R2.fq.gz	fastq fastq	1091293200.0	3637644.0	GSM8578760 r1	0:150 1:150	A:265519561;C:288647650;G:279105515;T:258001510;N:18964	150	150	265519561	288647650	279105515	258001510	18964	SRX26416444	SRS22936298	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34024	34024	SRR31031015	SRX26416443	SRS22936296	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES MALAT1 Rep4 minus	GSM8578759	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF NES MALAT1 Rep4 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578759	GSM8578759: ZF NES MALAT1 Rep4 minus; Danio rerio; OTHER	GSM8578759 r1	GSM8578759	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_MALAT1_Rep4_minus.R1.fq.gz ZF_NES_MALAT1_Rep4_minus.R2.fq.gz	fastq fastq	1395963600.0	4653212.0	GSM8578759 r1	0:150 1:150	A:339654289;C:369433701;G:356957685;T:329893853;N:24072	150	150	339654289	369433701	356957685	329893853	24072	SRX26416443	SRS22936296	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34025	34025	SRR31031016	SRX26416442	SRS22936295	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES MALAT1 Rep3 plus	GSM8578758	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF NES MALAT1 Rep3 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578758	GSM8578758: ZF NES MALAT1 Rep3 plus; Danio rerio; OTHER	GSM8578758 r1	GSM8578758	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_MALAT1_Rep3_plus.R1.fq.gz ZF_NES_MALAT1_Rep3_plus.R2.fq.gz	fastq fastq	1556195100.0	5187317.0	GSM8578758 r1	0:150 1:150	A:378553535;C:411730281;G:398086882;T:367797563;N:26839	150	150	378553535	411730281	398086882	367797563	26839	SRX26416442	SRS22936295	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34026	34026	SRR31031017	SRX26416441	SRS22936294	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES MALAT1 Rep3 minus	GSM8578757	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF NES MALAT1 Rep3 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578757	GSM8578757: ZF NES MALAT1 Rep3 minus; Danio rerio; OTHER	GSM8578757 r1	GSM8578757	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_MALAT1_Rep3_minus.R1.fq.gz ZF_NES_MALAT1_Rep3_minus.R2.fq.gz	fastq fastq	1511328900.0	5037763.0	GSM8578757 r1	0:150 1:150	A:367639521;C:400036694;G:386523395;T:357103340;N:25950	150	150	367639521	400036694	386523395	357103340	25950	SRX26416441	SRS22936294	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34027	34027	SRR31031018	SRX26416440	SRS22936293	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES MALAT1 Rep2 plus	GSM8578756	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF NES MALAT1 Rep2 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578756	GSM8578756: ZF NES MALAT1 Rep2 plus; Danio rerio; OTHER	GSM8578756 r1	GSM8578756	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_MALAT1_Rep2_plus.R1.fq.gz ZF_NES_MALAT1_Rep2_plus.R2.fq.gz	fastq fastq	1451137800.0	4837126.0	GSM8578756 r1	0:150 1:150	A:353052445;C:383981771;G:371154128;T:342925275;N:24181	150	150	353052445	383981771	371154128	342925275	24181	SRX26416440	SRS22936293	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34028	34028	SRR31031019	SRX26416439	SRS22936292	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES MALAT1 Rep2 minus	GSM8578755	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF NES MALAT1 Rep2 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578755	GSM8578755: ZF NES MALAT1 Rep2 minus; Danio rerio; OTHER	GSM8578755 r1	GSM8578755	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_MALAT1_Rep2_minus.R1.fq.gz ZF_NES_MALAT1_Rep2_minus.R2.fq.gz	fastq fastq	1286489400.0	4288298.0	GSM8578755 r1	0:150 1:150	A:312986127;C:340482608;G:329001591;T:303997982;N:21092	150	150	312986127	340482608	329001591	303997982	21092	SRX26416439	SRS22936292	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34029	34029	SRR31031020	SRX26416438	SRS22936291	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES MALAT1 Rep1 plus	GSM8578754	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF NES MALAT1 Rep1 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578754	GSM8578754: ZF NES MALAT1 Rep1 plus; Danio rerio; OTHER	GSM8578754 r1	GSM8578754	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_MALAT1_Rep1_plus.R1.fq.gz ZF_NES_MALAT1_Rep1_plus.R2.fq.gz	fastq fastq	1146380100.0	3821267.0	GSM8578754 r1	0:150 1:150	A:278826422;C:303464534;G:293239572;T:270830265;N:19307	150	150	278826422	303464534	293239572	270830265	19307	SRX26416438	SRS22936291	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34030	34030	SRR31031021	SRX26416437	SRS22936289	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES MALAT1 Rep1 minus	GSM8578753	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF\|geo loc name:missing\|collection date:missing	ZF NES MALAT1 Rep1 minus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:minus DBF	GSM8578753	GSM8578753: ZF NES MALAT1 Rep1 minus; Danio rerio; OTHER	GSM8578753 r1	GSM8578753	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_MALAT1_Rep1_minus.R1.fq.gz ZF_NES_MALAT1_Rep1_minus.R2.fq.gz	fastq fastq	1149087000.0	3830290.0	GSM8578753 r1	0:150 1:150	A:279487473;C:304130198;G:293947979;T:271501018;N:20332	150	150	279487473	304130198	293947979	271501018	20332	SRX26416437	SRS22936289	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
34031	34031	SRR31031022	SRX26416436	SRS22936290	SRP539182	PRJNA1174121	Quantification of subcellular RNA localization through direct detection of RNA oxidation	GSE279714	Other	Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.	pubmed:39605352;pubmed:40037712	ZF NES GAPDH Rep4 plus	GSM8578752	source name:2 dpf embryos\|tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF\|geo loc name:missing\|collection date:missing	ZF NES GAPDH Rep4 plus	OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.	2 dpf embryos		RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.	HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.	tissue:2 dpf embryos\|genotype:Halo NES\|treatment:plus DBF	GSM8578752	GSM8578752: ZF NES GAPDH Rep4 plus; Danio rerio; OTHER	GSM8578752 r1	GSM8578752	1	RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP539182	ZF_NES_GAPDH_Rep4_plus.R1.fq.gz ZF_NES_GAPDH_Rep4_plus.R2.fq.gz	fastq fastq	1010253300.0	3367511.0	GSM8578752 r1	0:150 1:150	A:264284161;C:228880831;G:244038984;T:273032130;N:17194	150	150	264284161	228880831	244038984	273032130	17194	SRX26416436	SRS22936290	SRA1993027	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus	Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	lexogen	bulk	unknown	unknown	United States	2024-10-17	Hatching	Embryo	Embryo Imprecise	All anatomical structures
42000	42000	SRR5379364	SRX2674572	SRS2073700	SRP102513	PRJNA380609	Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing	GSE97067	Other	DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.	pubmed:29636379	ddx39a 24hpf RIPseq	GSM2550918	source name:embryos\|genotype:ddx39a mutant\|tissue:embryo\|developmental stage:24hpf	ddx39a 24hpf RIPseq	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	embryos		Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		genotype:ddx39a mutant\|tissue:embryo\|developmental stage:24hpf	GSM2550918	GSM2550918: ddx39a 24hpf RIPseq; Danio rerio; RIP Seq	GSM2550918		1	Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2550918	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP102513	RDWHDANwwwCAABRAAPEI-206_1.fq.gz RDWHDANwwwCAABRAAPEI-206_2.fq.gz	fastq fastq	3819239400.0	19096197.0	GSM2550918 r1	0:100 1:100	A:751858949;C:1169790479;G:1139713624;T:756987876;N:888472	100	100	751858949	1169790479	1139713624	756987876	888472	SRX2674572	SRS2073700	SRA549449	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.98659	0.98572	0.28836	0.28975	0.89422	0.89558	0.75396	0.78553	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-03-27	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
42001	42001	SRR5379363	SRX2674571	SRS2073697	SRP102513	PRJNA380609	Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing	GSE97067	Other	DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.	pubmed:29636379	WT 24hpf RIPseq	GSM2550917	source name:embryos\|genotype:wild type\|tissue:embryo\|developmental stage:24hpf	WT 24hpf RIPseq	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	embryos		Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		genotype:wild type\|tissue:embryo\|developmental stage:24hpf	GSM2550917	GSM2550917: WT 24hpf RIPseq; Danio rerio; RIP Seq	GSM2550917		1	Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2550917	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP102513	RDWHDANwwwCAAARAAPEI-205_2.fq.gz RDWHDANwwwCAAARAAPEI-205_1.fq.gz	fastq fastq	3802882200.0	19014411.0	GSM2550917 r1	0:100 1:100	A:733911232;C:1178365174;G:1154031422;T:735690235;N:884137	100	100	733911232	1178365174	1154031422	735690235	884137	SRX2674571	SRS2073697	SRA549449	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.9866	0.98469	0.30567	0.30486	0.90796	0.90928	0.82926	0.83029	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-03-27	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
43458	43458	SRR5952027	SRX3110521	SRS2445614	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IP HCtranslatome RNAseq rep3	GSM2747294	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	IP HCtranslatome RNAseq rep3	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	GSM2747294	GSM2747294: IP HCtranslatome RNAseq rep3; Danio rerio; RIP Seq	GSM2747294		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747294	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900	RiboZF_IP4_R1.fastq.gz RiboZF_IP4_R2.fastq.gz	fastq fastq	4994833580.0	33330363.0	GSM2747294 r1	0:74.96 1:74.90	A:1202677579;C:1288784412;G:1278463604;T:1223941397;N:966588	74	74	1202677579	1288784412	1278463604	1223941397	966588	SRX3110521	SRS2445614	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.61854	0.6151	0.20328	0.19651	0.83599	0.84104	0.60632	0.59954	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Embryo Imprecise	All anatomical structures
43459	43459	SRR5952026	SRX3110520	SRS2445613	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IP HCtranslatome RNAseq rep2	GSM2747293	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	IP HCtranslatome RNAseq rep2	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	GSM2747293	GSM2747293: IP HCtranslatome RNAseq rep2; Danio rerio; RIP Seq	GSM2747293		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747293	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900	RiboZF_IP2_R1.fastq.gz RiboZF_IP2_R2.fastq.gz	fastq fastq	4530855300.0	30205702.0	GSM2747293 r1	0:75 1:75	A:1112381418;C:1153277132;G:1147183468;T:1117133915;N:879367	75	75	1112381418	1153277132	1147183468	1117133915	879367	SRX3110520	SRS2445613	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.64948	0.64878	0.15967	0.15683	0.80756	0.81288	0.56438	0.56275	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Embryo Imprecise	All anatomical structures
43460	43460	SRR5952025	SRX3110519	SRS2445612	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IP HCtranslatome RNAseq rep1	GSM2747292	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	IP HCtranslatome RNAseq rep1	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	GSM2747292	GSM2747292: IP HCtranslatome RNAseq rep1; Danio rerio; RIP Seq	GSM2747292		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747292	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900	RiboZF_IP1_R1.fastq.gz RiboZF_IP1_R2.fastq.gz	fastq fastq	5261113350.0	35074089.0	GSM2747292 r1	0:75 1:75	A:1356848229;C:1276483567;G:1260001700;T:1366757927;N:1021927	75	75	1356848229	1276483567	1260001700	1366757927	1021927	SRX3110519	SRS2445612	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.66363	0.6599	0.15644	0.15316	0.76808	0.7725	0.48538	0.48933	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Embryo Imprecise	All anatomical structures
47735	47735	SRR6846413	SRX3801804	SRS3053760	SRP135842	PRJNA438572	RNA seq of embryo stimulated by interferons in Danio rerio	PRJNA438572	Other	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			IFNY	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:stimulated by interferons\|sex:missing\|tissue:embryo\|collection date:2017 03 12\|geo loc name:China:Wuhan\|BioSampleModel:Model organism or animal									RNA seq of embryo stimulated by interferons in Danio rerio	IFNY	IFNY	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP135842	IFNY_S13_L004_R2_001.fastq.gz IFNY_S13_L004_R1_001.fastq.gz	fastq fastq	8611053142.0	28513421.0	IFNY S13 L004 R1 001.fastq.gz	0:151 1:151	A:2172756042;C:2133682578;G:2133331951;T:2170977207;N:305364	151	151	2172756042	2133682578	2133331951	2170977207	305364	SRX3801804	SRS3053760	SRA666995	Chinese Academy of Sciences\|Institute of Hydrobiology	Chinese Academy of Sciences	2	0.955	0.95804	0.04308	0.04392	0.70218	0.71033	0.46525	0.462	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2018-03-16	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
47736	47736	SRR6846414	SRX3801803	SRS3053759	SRP135842	PRJNA438572	RNA seq of embryo stimulated by interferons in Danio rerio	PRJNA438572	Other	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			vector	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:stimulated by interferons\|sex:missing\|tissue:embryo\|collection date:2017 03 11\|geo loc name:China:Wuhan\|BioSampleModel:Model organism or animal									RNA seq of embryo stimulated by interferons in Danio rerio	vector	vector	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP135842	vector_S12_L004_R1_001.fastq.gz vector_S12_L004_R2_001.fastq.gz	fastq fastq	10279577472.0	34038336.0	vector S12 L004 R1 001.fastq.gz	0:151 1:151	A:2615896150;C:2524788585;G:2528030423;T:2610500306;N:362008	151	151	2615896150	2524788585	2528030423	2610500306	362008	SRX3801803	SRS3053759	SRA666995	Chinese Academy of Sciences\|Institute of Hydrobiology	Chinese Academy of Sciences	2	0.9555	0.9579	0.04617	0.04728	0.70337	0.71072	0.46191	0.46954	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2018-03-16	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
47737	47737	SRR6846415	SRX3801802	SRS3053756	SRP135842	PRJNA438572	RNA seq of embryo stimulated by interferons in Danio rerio	PRJNA438572	Other	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			IFNG	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:stimulated by interferons\|sex:missing\|tissue:embryo\|collection date:2017 03 14\|geo loc name:China:Wuhan\|BioSampleModel:Model organism or animal									RNA seq of embryo stimulated by interferons in Danio rerio	IFNG	IFNG	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP135842	IFNG_S15_L004_R1_001.fastq.gz IFNG_S15_L004_R2_001.fastq.gz	fastq fastq	9082411722.0	30074211.0	IFNG S15 L004 R2 001.fastq.gz	0:151 1:151	A:2283553036;C:2258886090;G:2257807913;T:2281843116;N:321567	151	151	2283553036	2258886090	2257807913	2281843116	321567	SRX3801802	SRS3053756	SRA666995	Chinese Academy of Sciences\|Institute of Hydrobiology	Chinese Academy of Sciences	2	0.95442	0.95794	0.03954	0.04042	0.70694	0.71674	0.45987	0.45045	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2021-01-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
47738	47738	SRR6846416	SRX3801801	SRS3053758	SRP135842	PRJNA438572	RNA seq of embryo stimulated by interferons in Danio rerio	PRJNA438572	Other	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			IFN1	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:stimulated by interferons\|sex:missing\|tissue:embryo\|collection date:2017 03 13\|geo loc name:China:Wuhan\|BioSampleModel:Model organism or animal									RNA seq of embryo stimulated by interferons in Danio rerio	IFN1	IFN1	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP135842	IFN1_S14_L004_R1_001.fastq.gz IFN1_S14_L004_R2_001.fastq.gz	fastq fastq	9801986820.0	32456910.0	IFN1 S14 L004 R2 001.fastq.gz	0:151 1:151	A:2476732153;C:2426531434;G:2425138255;T:2473239913;N:345065	151	151	2476732153	2426531434	2425138255	2473239913	345065	SRX3801801	SRS3053758	SRA666995	Chinese Academy of Sciences\|Institute of Hydrobiology	Chinese Academy of Sciences	2	0.95422	0.9559	0.0427	0.04366	0.7068	0.71467	0.45683	0.46354	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2021-01-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
47739	47739	SRR6846417	SRX3801800	SRS3053757	SRP135842	PRJNA438572	RNA seq of embryo stimulated by interferons in Danio rerio	PRJNA438572	Other	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			IFN3	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:stimulated by interferons\|sex:missing\|tissue:embryo\|collection date:2017 03 15\|geo loc name:China:Wuhan\|BioSampleModel:Model organism or animal									RNA seq of embryo stimulated by interferons in Danio rerio	IFN3	IFN3	RNA seq of embryo stimulated by interferons in Danio rerio provides transcriptome data which affords a unique view for understanding differences of expression of ISGs regulated by different interferons.			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP135842	IFN3_S16_L004_R2_001.fastq.gz IFN3_S16_L004_R1_001.fastq.gz	fastq fastq	8628116746.0	28569923.0	IFN3 S16 L004 R2 001.fastq.gz	0:151 1:151	A:2178313667;C:2137778611;G:2137088678;T:2174631627;N:304163	151	151	2178313667	2137778611	2137088678	2174631627	304163	SRX3801800	SRS3053757	SRA666995	Chinese Academy of Sciences\|Institute of Hydrobiology	Chinese Academy of Sciences	2	0.95589	0.95838	0.04186	0.04249	0.70587	0.71376	0.44245	0.46157	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2021-01-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
49573	49573	SRR10434662	SRX7130632	SRS5639976	SRP163087	PRJNA494251	Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis	GSE120724	Other	We resolved the RNA secondary structure during zebrafish early embryogenesis based on in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages. Also we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2 4 6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.	pubmed:32423473	shield Flag Elavl1a iCLIP rep2	GSM4157939	tissue:zebrafish embryos\|strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:6hpf	shield Flag Elavl1a iCLIP rep2	The proceesing procedure is similar to CTK toolhttps://zhanglab.c2b2.columbia.edu/index.php/ICLIP data analysis using CTK. First we trimmed three prime adaptor from reads by cutadapt collapsed duplicated reads by fastq2collapse.pl in CTK tool stripped 5’ degenerated barcode mapped clean reads to zebrafish reference genomez10 by bwav0.7.17. data from replicates was merged for peak calling We use CTK tool CITS mode to call the peaks. Reads were clustered using tag2cluster.pl with parameters big s maxgap " 1" peaks are identified using tag2peak.pl with parameters big ss v prefix "CITS" gap 25 p 0.05 Genome build: z10 Supplementary files format and content: iCLIP peaks identified by CTK tool were provided in bed file format. The first three columns represent the 0 based location of the peak in the genome and the last column represents the strand.The fourth column reprents the peak ID and describes the gene locus peak heightPH expected PH/backgroundPH0 and pvalueP. The fifth column represents the peak height.	zebrafish embryos		iCLIP seq was carried out as previously described Despic et al. 2017. Breifly flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc	Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.	strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:6hpf	GSM4157939	GSM4157939: shield Flag Elavl1a iCLIP rep2; Danio rerio; OTHER	GSM4157939		1	iCLIP seq was carried out as previously described Despic et al. 2017. Breifly flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM4157939	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP163087	Shield_Elavl1a_iCLIP_rep2.R2.fq.gz Shield_Elavl1a_iCLIP_rep2.R1.fq.gz	fastq fastq	23879342400.0	79597808.0	GSM4157939 r1	0:150 1:150	A:6335254303;C:5166953187;G:6017120995;T:6358132998;N:1880917	150	150	6335254303	5166953187	6017120995	6358132998	1880917	SRX7130632	SRS5639976	SRA787572	GEO	Life Science, Tsinghua University	2	0.14294	0.15151	0.03583	0.08959	0.99397	0.98269	0.96727	0.75507	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	smarter	bulk	clip	iclip	China	2019-11-12	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
49574	49574	SRR10434661	SRX7130631	SRS5639975	SRP163087	PRJNA494251	Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis	GSE120724	Other	We resolved the RNA secondary structure during zebrafish early embryogenesis based on in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages. Also we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2 4 6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.	pubmed:32423473	shield Flag Elavl1a iCLIP rep1	GSM4157938	tissue:zebrafish embryos\|strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:6hpf	shield Flag Elavl1a iCLIP rep1	The proceesing procedure is similar to CTK toolhttps://zhanglab.c2b2.columbia.edu/index.php/ICLIP data analysis using CTK. First we trimmed three prime adaptor from reads by cutadapt collapsed duplicated reads by fastq2collapse.pl in CTK tool stripped 5’ degenerated barcode mapped clean reads to zebrafish reference genomez10 by bwav0.7.17. data from replicates was merged for peak calling We use CTK tool CITS mode to call the peaks. Reads were clustered using tag2cluster.pl with parameters big s maxgap " 1" peaks are identified using tag2peak.pl with parameters big ss v prefix "CITS" gap 25 p 0.05 Genome build: z10 Supplementary files format and content: iCLIP peaks identified by CTK tool were provided in bed file format. The first three columns represent the 0 based location of the peak in the genome and the last column represents the strand.The fourth column reprents the peak ID and describes the gene locus peak heightPH expected PH/backgroundPH0 and pvalueP. The fifth column represents the peak height.	zebrafish embryos		iCLIP seq was carried out as previously described Despic et al. 2017. Breifly flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc	Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.	strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:6hpf	GSM4157938	GSM4157938: shield Flag Elavl1a iCLIP rep1; Danio rerio; OTHER	GSM4157938		1	iCLIP seq was carried out as previously described Despic et al. 2017. Breifly flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM4157938	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP163087	Shield_Elavl1a_iCLIP_rep1.R1.fq.gz Shield_Elavl1a_iCLIP_rep1.R2.fq.gz	fastq fastq	22375977600.0	74586592.0	GSM4157938 r1	0:150 1:150	A:6243025236;C:5008499337;G:5418170547;T:5704514909;N:1767571	150	150	6243025236	5008499337	5418170547	5704514909	1767571	SRX7130631	SRS5639975	SRA787572	GEO	Life Science, Tsinghua University	2	0.05144	0.12625	0.01219	0.09577	0.99734	0.98113	0.8629	0.52429	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	full_length	poly_a	smarter	bulk	clip	iclip	China	2019-11-12	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
49575	49575	SRR10434660	SRX7130630	SRS5639974	SRP163087	PRJNA494251	Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis	GSE120724	Other	We resolved the RNA secondary structure during zebrafish early embryogenesis based on in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages. Also we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2 4 6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.	pubmed:32423473	sphere Flag Elavl1a iCLIP rep2	GSM4157937	tissue:zebrafish embryos\|strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:4hpf	sphere Flag Elavl1a iCLIP rep2	The proceesing procedure is similar to CTK toolhttps://zhanglab.c2b2.columbia.edu/index.php/ICLIP data analysis using CTK. First we trimmed three prime adaptor from reads by cutadapt collapsed duplicated reads by fastq2collapse.pl in CTK tool stripped 5’ degenerated barcode mapped clean reads to zebrafish reference genomez10 by bwav0.7.17. data from replicates was merged for peak calling We use CTK tool CITS mode to call the peaks. Reads were clustered using tag2cluster.pl with parameters big s maxgap " 1" peaks are identified using tag2peak.pl with parameters big ss v prefix "CITS" gap 25 p 0.05 Genome build: z10 Supplementary files format and content: iCLIP peaks identified by CTK tool were provided in bed file format. The first three columns represent the 0 based location of the peak in the genome and the last column represents the strand.The fourth column reprents the peak ID and describes the gene locus peak heightPH expected PH/backgroundPH0 and pvalueP. The fifth column represents the peak height.	zebrafish embryos		iCLIP seq was carried out as previously described Despic et al. 2017. Breifly flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc	Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.	strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:4hpf	GSM4157937	GSM4157937: sphere Flag Elavl1a iCLIP rep2; Danio rerio; OTHER	GSM4157937		1	iCLIP seq was carried out as previously described Despic et al. 2017. Breifly flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM4157937	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP163087	Sphere_Elavl1a_iCLIP_rep2.R1.fq.gz Sphere_Elavl1a_iCLIP_rep2.R2.fq.gz	fastq fastq	22090855200.0	73636184.0	GSM4157937 r1	0:150 1:150	A:5631298996;C:5114935575;G:5742247735;T:5600647498;N:1725396	150	150	5631298996	5114935575	5742247735	5600647498	1725396	SRX7130630	SRS5639974	SRA787572	GEO	Life Science, Tsinghua University	2	0.23476	0.17586	0.06861	0.08859	0.99563	0.98873	0.95465	0.79994	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	full_length	poly_a	smarter	bulk	clip	iclip	China	2019-11-12	Blastula	Embryo	Embryo Imprecise	All anatomical structures
49576	49576	SRR10434659	SRX7130629	SRS5639973	SRP163087	PRJNA494251	Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis	GSE120724	Other	We resolved the RNA secondary structure during zebrafish early embryogenesis based on in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages. Also we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2 4 6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.	pubmed:32423473	sphere Flag Elavl1a iCLIP rep1	GSM4157936	tissue:zebrafish embryos\|strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:4hpf	sphere Flag Elavl1a iCLIP rep1	The proceesing procedure is similar to CTK toolhttps://zhanglab.c2b2.columbia.edu/index.php/ICLIP data analysis using CTK. First we trimmed three prime adaptor from reads by cutadapt collapsed duplicated reads by fastq2collapse.pl in CTK tool stripped 5’ degenerated barcode mapped clean reads to zebrafish reference genomez10 by bwav0.7.17. data from replicates was merged for peak calling We use CTK tool CITS mode to call the peaks. Reads were clustered using tag2cluster.pl with parameters big s maxgap " 1" peaks are identified using tag2peak.pl with parameters big ss v prefix "CITS" gap 25 p 0.05 Genome build: z10 Supplementary files format and content: iCLIP peaks identified by CTK tool were provided in bed file format. The first three columns represent the 0 based location of the peak in the genome and the last column represents the strand.The fourth column reprents the peak ID and describes the gene locus peak heightPH expected PH/backgroundPH0 and pvalueP. The fifth column represents the peak height.	zebrafish embryos		iCLIP seq was carried out as previously described Despic et al. 2017. Breifly flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc	Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.	strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:4hpf	GSM4157936	GSM4157936: sphere Flag Elavl1a iCLIP rep1; Danio rerio; OTHER	GSM4157936		1	iCLIP seq was carried out as previously described Despic et al. 2017. Breifly flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM4157936	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP163087	Sphere_Elavl1a_iCLIP_rep1.R2.fq.gz Sphere_Elavl1a_iCLIP_rep1.R1.fq.gz	fastq fastq	15794202300.0	52647341.0	GSM4157936 r1	0:150 1:150	A:4443931911;C:3527112429;G:3707720167;T:4114188890;N:1248903	150	150	4443931911	3527112429	3707720167	4114188890	1248903	SRX7130629	SRS5639973	SRA787572	GEO	Life Science, Tsinghua University	2	0.06877	0.10388	0.02139	0.07135	0.99776	0.98413	0.87145	0.57456	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	full_length	poly_a	smarter	bulk	clip	iclip	China	2019-11-12	Blastula	Embryo	Embryo Imprecise	All anatomical structures
54307	54307	SRR10129555	SRX6857975	SRS5395856	SRP221863	PRJNA565584	The functions of igf2bp3 during zebrafish early development	PRJNA565584	Whole Genome Sequencing	RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.		Model organism or animal sample from Danio rerio	RIP seq zebrafish embryo HA rabbit	strain:AB\|dev stage:embryo\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal									RIP seq zebrafish embryo sphere HA	HA sphere	HA sphere	RIP seq			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP221863	IP2_R1.fq.gz IP2_R2.fq.gz	fastq fastq	7528561800.0	25095206.0	IP2 R1.fq.gz	0:150 1:150	A:1638987252;C:1830922014;G:2628590112;T:1430016657;N:45765	150	150	1638987252	1830922014	2628590112	1430016657	45765	SRX6857975	SRS5395856	SRA962995	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.92316	0.96332	0.32571	0.34771	0.89173	0.88962	0.89557	0.89793	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2019-09-17	Blastula	Embryo	Embryo Imprecise	All anatomical structures
54308	54308	SRR10129346	SRX6857766	SRS5395649	SRP221863	PRJNA565584	The functions of igf2bp3 during zebrafish early development	PRJNA565584	Whole Genome Sequencing	RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.		Model organism or animal sample from Danio rerio	RIP seq zebrafish embryo IgG rabbit	strain:AB\|dev stage:embryo\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal									RIP seq zebrafish embryo sphere IgG	IgG sphere	IgG sphere	RIP seq			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP221863	IgG1_R1.fq.gz IgG1_R2.fq.gz	fastq fastq	2647374600.0	8824582.0	IgG1 R1.fq.gz	0:150 1:150	A:565620765;C:650153559;G:936592543;T:494992101;N:15632	150	150	565620765	650153559	936592543	494992101	15632	SRX6857766	SRS5395649	SRA962944	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.95349	0.96423	0.33504	0.34458	0.93748	0.93726	0.85176	0.91118	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2019-09-17	Blastula	Embryo	Embryo Imprecise	All anatomical structures
56341	56341	SRR10948891	SRX7615949	SRS6049208	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	Prim5 Cyt CAGE	GSM4278497	source name:24hpf stage embryo\|tissue:zebrafish embryos\|Stage:24hpf\|fraction:Cytosolic\|molecule type:capped RNAs	Prim5 Cyt CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	24hpf stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:24hpf\|fraction:Cytosolic\|molecule type:capped RNAs	GSM4278497	GSM4278497: Prim5 Cyt CAGE; Danio rerio; OTHER	GSM4278497		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278497	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Prim5_Cyt_L006_R1_001.fastq.gz Prim5_Cyt_L006_R2_001.fastq.gz	fastq fastq	11647548055.0	122605769.0	GSM4278497 r1	0:51 1:44	A:2440692679;C:3082646191;G:3382532043;T:2741423146;N:253996	51	44	2440692679	3082646191	3382532043	2741423146	253996	SRX7615949	SRS6049208	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.98284	0.34054	0.34811	0.12661	0.90753	0.95018	0.67956	0.71841	51	44	B	T	mate2 technical by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
56342	56342	SRR10948890	SRX7615948	SRS6049207	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	Prim5 Nuc CAGE	GSM4278496	source name:24hpf stage embryo\|tissue:zebrafish embryos\|Stage:24hpf\|fraction:Nuclear\|molecule type:capped RNAs	Prim5 Nuc CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	24hpf stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:24hpf\|fraction:Nuclear\|molecule type:capped RNAs	GSM4278496	GSM4278496: Prim5 Nuc CAGE; Danio rerio; OTHER	GSM4278496		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278496	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Prim5_Nuc_L006_R1_001.fastq.gz Prim5_Nuc_L006_R2_001.fastq.gz	fastq fastq	2052983345.0	21610351.0	GSM4278496 r1	0:51 1:44	A:448698187;C:513165511;G:563783876;T:527290561;N:45210	51	44	448698187	513165511	563783876	527290561	45210	SRX7615948	SRS6049207	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.95137	0.36483	0.38701	0.1658	0.82292	0.90638	0.65602	0.68468	51	44	B	T	mate2 technical by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
56343	56343	SRR10948889	SRX7615947	SRS6049205	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	Shield Cyt CAGE	GSM4278495	source name:Shield stage embryo\|tissue:zebrafish embryos\|Stage:Shield\|fraction:Cytosolic\|molecule type:capped RNAs	Shield Cyt CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	Shield stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:Shield\|fraction:Cytosolic\|molecule type:capped RNAs	GSM4278495	GSM4278495: Shield Cyt CAGE; Danio rerio; OTHER	GSM4278495		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278495	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Shield_Cyt_L006_R1_001.fastq.gz Shield_Cyt_L006_R2_001.fastq.gz	fastq fastq	8704643185.0	91627823.0	GSM4278495 r1	0:51 1:44	A:1930221949;C:2128885351;G:2388442525;T:2256907064;N:186296	51	44	1930221949	2128885351	2388442525	2256907064	186296	SRX7615947	SRS6049205	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.89389	0.40438	0.14385	0.06093	0.78792	0.8352	0.5381	0.52296	51	44	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56344	56344	SRR10948888	SRX7615946	SRS6049206	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	Shield Nuc CAGE	GSM4278494	source name:Shield stage embryo\|tissue:zebrafish embryos\|Stage:Shield\|fraction:Nuclear\|molecule type:capped RNAs	Shield Nuc CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	Shield stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:Shield\|fraction:Nuclear\|molecule type:capped RNAs	GSM4278494	GSM4278494: Shield Nuc CAGE; Danio rerio; OTHER	GSM4278494		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278494	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Shield_Nuc_L006_R1_001.fastq.gz Shield_Nuc_L006_R2_001.fastq.gz	fastq fastq	1700102330.0	17895814.0	GSM4278494 r1	0:51 1:44	A:370009933;C:422952763;G:478245997;T:428857334;N:36303	51	44	370009933	422952763	478245997	428857334	36303	SRX7615946	SRS6049206	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.9163	0.35706	0.26264	0.1183	0.78244	0.863	0.6044	0.56423	51	44	B	T	mate2 technical by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56345	56345	SRR10948887	SRX7615945	SRS6049203	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	Dome Cyt CAGE	GSM4278493	source name:Dome stage embryo\|tissue:zebrafish embryos\|Stage:Dome\|fraction:Cytosolic\|molecule type:capped RNAs	Dome Cyt CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	Dome stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:Dome\|fraction:Cytosolic\|molecule type:capped RNAs	GSM4278493	GSM4278493: Dome Cyt CAGE; Danio rerio; OTHER	GSM4278493		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278493	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Dome_Cyt_L006_R1_001.fastq.gz Dome_Cyt_L006_R2_001.fastq.gz	fastq fastq	2925028910.0	30789778.0	GSM4278493 r1	0:51 1:44	A:640538932;C:732480084;G:812849999;T:739097218;N:62677	51	44	640538932	732480084	812849999	739097218	62677	SRX7615945	SRS6049203	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.91	0.37548	0.19179	0.07754	0.77849	0.8296	0.5771	0.54047	51	44	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
56346	56346	SRR10948886	SRX7615944	SRS6049204	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	Dome Nuc CAGE	GSM4278492	source name:Dome stage embryo\|tissue:zebrafish embryos\|Stage:Dome\|fraction:Nuclear\|molecule type:capped RNAs	Dome Nuc CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	Dome stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:Dome\|fraction:Nuclear\|molecule type:capped RNAs	GSM4278492	GSM4278492: Dome Nuc CAGE; Danio rerio; OTHER	GSM4278492		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278492	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Dome_Nuc_L006_R1_001.fastq.gz Dome_Nuc_L006_R2_001.fastq.gz	fastq fastq	1025349630.0	10793154.0	GSM4278492 r1	0:51 1:44	A:224542517;C:258091485;G:286132413;T:256561363;N:21852	51	44	224542517	258091485	286132413	256561363	21852	SRX7615944	SRS6049204	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.90004	0.35498	0.26716	0.1319	0.75256	0.84053	0.59032	0.58429	51	44	B	T	mate2 technical by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
56347	56347	SRR10948885	SRX7615943	SRS6049202	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	1000Cell Cyt CAGE	GSM4278491	source name:1000Cell stage embryo\|tissue:zebrafish embryos\|Stage:1000Cell\|fraction:Cytosolic\|molecule type:capped RNAs	1000Cell Cyt CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	1000Cell stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:1000Cell\|fraction:Cytosolic\|molecule type:capped RNAs	GSM4278491	GSM4278491: 1000Cell Cyt CAGE; Danio rerio; OTHER	GSM4278491		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278491	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Cell1000_Cyt_L006_R2_001.fastq.gz Cell1000_Cyt_L006_R1_001.fastq.gz	fastq fastq	2221341870.0	23382546.0	GSM4278491 r1	0:51 1:44	A:463771517;C:578169553;G:636288303;T:543065256;N:47241	51	44	463771517	578169553	636288303	543065256	47241	SRX7615943	SRS6049202	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.95318	0.36797	0.24288	0.09383	0.78654	0.83493	0.6438	0.56785	51	44	B	T	mate2 technical by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
56348	56348	SRR10948884	SRX7615942	SRS6049201	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	1000Cell Nuc CAGE	GSM4278490	source name:1000Cell stage embryo\|tissue:zebrafish embryos\|Stage:1000Cell\|fraction:Nuclear\|molecule type:capped RNAs	1000Cell Nuc CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	1000Cell stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:1000Cell\|fraction:Nuclear\|molecule type:capped RNAs	GSM4278490	GSM4278490: 1000Cell Nuc CAGE; Danio rerio; OTHER	GSM4278490		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278490	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Cell1000_Nuc_L006_R1_001.fastq.gz Cell1000_Nuc_L006_R2_001.fastq.gz	fastq fastq	1165749750.0	12271050.0	GSM4278490 r1	0:51 1:44	A:242410646;C:306083126;G:336746651;T:280484368;N:24959	51	44	242410646	306083126	336746651	280484368	24959	SRX7615942	SRS6049201	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.91201	0.3374	0.28385	0.1085	0.78031	0.84857	0.66929	0.60831	51	44	B	T	mate2 technical by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
56349	56349	SRR10948883	SRX7615941	SRS6049200	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	256Cell Cyt CAGE	GSM4278489	source name:256Cell stage embryo\|tissue:zebrafish embryos\|Stage:256Cell\|fraction:Cytosolic\|molecule type:capped RNAs	256Cell Cyt CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	256Cell stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:256Cell\|fraction:Cytosolic\|molecule type:capped RNAs	GSM4278489	GSM4278489: 256Cell Cyt CAGE; Danio rerio; OTHER	GSM4278489		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278489	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Cell256_Cyt_L006_R1_001.fastq.gz Cell256_Cyt_L006_R2_001.fastq.gz	fastq fastq	730451200.0	7688960.0	GSM4278489 r1	0:51 1:44	A:149831122;C:187919862;G:214702408;T:177982361;N:15447	51	44	149831122	187919862	214702408	177982361	15447	SRX7615941	SRS6049200	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.9505	0.36535	0.23886	0.09179	0.80474	0.84695	0.67208	0.61294	51	44	B	T	mate2 technical by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
56350	56350	SRR10948882	SRX7615940	SRS6049199	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	256Cell Nuc CAGE	GSM4278488	source name:256Cell stage embryo\|tissue:zebrafish embryos\|Stage:256Cell\|fraction:Nuclear\|molecule type:capped RNAs	256Cell Nuc CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	256Cell stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:256Cell\|fraction:Nuclear\|molecule type:capped RNAs	GSM4278488	GSM4278488: 256Cell Nuc CAGE; Danio rerio; OTHER	GSM4278488		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278488	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Cell256_Nuc_L006_R1_001.fastq.gz Cell256_Nuc_L006_R2_001.fastq.gz	fastq fastq	914411290.0	9625382.0	GSM4278488 r1	0:51 1:44	A:183085401;C:238593034;G:274558029;T:218155345;N:19481	51	44	183085401	238593034	274558029	218155345	19481	SRX7615940	SRS6049199	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.96805	0.36191	0.34605	0.11823	0.82351	0.86963	0.68965	0.64112	51	44	B	T	mate2 technical by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
56351	56351	SRR10948881	SRX7615939	SRS6049198	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	64Cell Cyt CAGE	GSM4278487	source name:64Cell stage embryo\|tissue:zebrafish embryos\|Stage:64Cell\|fraction:Cytosolic\|molecule type:capped RNAs	64Cell Cyt CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	64Cell stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:64Cell\|fraction:Cytosolic\|molecule type:capped RNAs	GSM4278487	GSM4278487: 64Cell Cyt CAGE; Danio rerio; OTHER	GSM4278487		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278487	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Cell64_Cyt_L006_R1_001.fastq.gz Cell64_Cyt_L006_R2_001.fastq.gz	fastq fastq	166574140.0	1753412.0	GSM4278487 r1	0:51 1:44	A:34424987;C:43748779;G:47831884;T:40564939;N:3551	51	44	34424987	43748779	47831884	40564939	3551	SRX7615939	SRS6049198	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.94853	0.36859	0.20547	0.07164	0.80377	0.84845	0.66429	0.60646	51	44	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
56352	56352	SRR10948880	SRX7615938	SRS6049197	SRP243873	PRJNA602610	Global promoter usage in the differentfractions of the cell during early zebrafish development	GSE144040	Other	We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome Shield and Prim 5 stages of development.	pubmed:33795334	64Cell Nuc CAGE	GSM4278486	source name:64Cell stage embryo\|tissue:zebrafish embryos\|Stage:64Cell\|fraction:Nuclear\|molecule type:capped RNAs	64Cell Nuc CAGE	Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering normalization removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al. 2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format	64Cell stage embryo	Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction.	RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.	tissue:zebrafish embryos\|Stage:64Cell\|fraction:Nuclear\|molecule type:capped RNAs	GSM4278486	GSM4278486: 64Cell Nuc CAGE; Danio rerio; OTHER	GSM4278486		1	RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis also called cap trapping method Carninci et al. 1996 targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.	GEO Accession:GSM4278486	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP243873	Cell64_Nuc_L006_R1_001.fastq.gz Cell64_Nuc_L006_R2_001.fastq.gz	fastq fastq	254581570.0	2679806.0	GSM4278486 r1	0:51 1:44	A:53351059;C:66480035;G:73184710;T:61560147;N:5619	51	44	53351059	66480035	73184710	61560147	5619	SRX7615938	SRS6049197	SRA1029879	GEO	School of Biosciences, University of Birmingham	2	0.85142	0.32881	0.18708	0.06992	0.7864	0.84159	0.62224	0.57075	51	44	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	5prime	other	unknown	bulk	unknown	unknown	United Kingdom	2020-01-22	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
60025	60025	SRR12103783	SRX8627954	SRS6916259	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB4 IP	GSM4644253	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	PCB4 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	GSM4644253	GSM4644253: PCB4 IP; Danio rerio; RIP Seq	GSM4644253		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644253	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	P4_m6A-IP_S16_R1_001.fastq.gz P4_m6A-IP_S16_R2_001.fastq.gz	fastq fastq	2309150560.0	15191780.0	GSM4644253 r1	0:76 1:76	A:490672579;C:656568819;G:666651729;T:495020365;N:237068	76	76	490672579	656568819	666651729	495020365	237068	SRX8627954	SRS6916259	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.94474	0.944	0.18094	0.18203	0.7515	0.75554	0.60771	0.6152	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60026	60026	SRR12103782	SRX8627953	SRS6916258	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB3 IP	GSM4644252	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	PCB3 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	GSM4644252	GSM4644252: PCB3 IP; Danio rerio; RIP Seq	GSM4644252		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644252	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	P3_m6A-IP_S15_R2_001.fastq.gz P3_m6A-IP_S15_R1_001.fastq.gz	fastq fastq	2965972504.0	19512977.0	GSM4644252 r1	0:76 1:76	A:620624207;C:853765538;G:874990332;T:616281897;N:310530	76	76	620624207	853765538	874990332	616281897	310530	SRX8627953	SRS6916258	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93433	0.93213	0.16543	0.16208	0.75043	0.753	0.62186	0.64359	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60027	60027	SRR12103781	SRX8627952	SRS6916257	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB2 IP	GSM4644251	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	PCB2 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	GSM4644251	GSM4644251: PCB2 IP; Danio rerio; RIP Seq	GSM4644251		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644251	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	P2_m6A-IP_S14_R2_001.fastq.gz P2_m6A-IP_S14_R1_001.fastq.gz	fastq fastq	2687973472.0	17684036.0	GSM4644251 r1	0:76 1:76	A:585901626;C:744255122;G:756993274;T:600539454;N:283996	76	76	585901626	744255122	756993274	600539454	283996	SRX8627952	SRS6916257	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.9445	0.94466	0.16876	0.17035	0.74728	0.75022	0.57878	0.57933	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60028	60028	SRR12103780	SRX8627951	SRS6916256	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB1 IP	GSM4644250	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	PCB1 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	GSM4644250	GSM4644250: PCB1 IP; Danio rerio; RIP Seq	GSM4644250		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644250	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	P1_m6A-IP_S13_R1_001.fastq.gz P1_m6A-IP_S13_R2_001.fastq.gz	fastq fastq	2596174288.0	17080094.0	GSM4644250 r1	0:76 1:76	A:564523297;C:723443207;G:735894528;T:572044392;N:268864	76	76	564523297	723443207	735894528	572044392	268864	SRX8627951	SRS6916256	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93494	0.93528	0.17469	0.17518	0.746	0.74803	0.60114	0.60005	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60029	60029	SRR12103779	SRX8627950	SRS6916255	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB4 Input	GSM4644249	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB4 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644249	GSM4644249: PCB4 Input; Danio rerio; RIP Seq	GSM4644249		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644249	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	P4_INPUT_S8_R1_001.fastq.gz P4_INPUT_S8_R2_001.fastq.gz	fastq fastq	3655473384.0	24049167.0	GSM4644249 r1	0:76 1:76	A:680110064;C:1145409769;G:1179103219;T:650470372;N:379960	76	76	680110064	1145409769	1179103219	650470372	379960	SRX8627950	SRS6916255	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93037	0.96319	0.21668	0.22563	0.86338	0.86385	0.77257	0.70059	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60030	60030	SRR12103778	SRX8627949	SRS6916254	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB3 Input	GSM4644248	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB3 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644248	GSM4644248: PCB3 Input; Danio rerio; RIP Seq	GSM4644248		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644248	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	P3_INPUT_S7_R1_001.fastq.gz P3_INPUT_S7_R2_001.fastq.gz	fastq fastq	4926238376.0	32409463.0	GSM4644248 r1	0:76 1:76	A:929043061;C:1530175131;G:1577898210;T:888604850;N:517124	76	76	929043061	1530175131	1577898210	888604850	517124	SRX8627949	SRS6916254	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92875	0.95698	0.21539	0.22073	0.85253	0.85431	0.76235	0.68659	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60031	60031	SRR12103777	SRX8627948	SRS6916253	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB2 Input	GSM4644247	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB2 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644247	GSM4644247: PCB2 Input; Danio rerio; RIP Seq	GSM4644247		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644247	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	P2_INPUT_S6_R1_001.fastq.gz P2_INPUT_S6_R2_001.fastq.gz	fastq fastq	5669611400.0	37300075.0	GSM4644247 r1	0:76 1:76	A:1050955836;C:1780355588;G:1829450728;T:1008257255;N:591993	76	76	1050955836	1780355588	1829450728	1008257255	591993	SRX8627948	SRS6916253	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93297	0.93791	0.21298	0.21667	0.85902	0.86302	0.7387	0.69759	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60032	60032	SRR12103776	SRX8627947	SRS6916252	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB1 Input	GSM4644246	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB1 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644246	GSM4644246: PCB1 Input; Danio rerio; RIP Seq	GSM4644246		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644246	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	P1_INPUT_S5_R1_001.fastq.gz P1_INPUT_S5_R2_001.fastq.gz	fastq fastq	4154972744.0	27335347.0	GSM4644246 r1	0:76 1:76	A:764769282;C:1310937656;G:1344287240;T:734545457;N:433109	76	76	764769282	1310937656	1344287240	734545457	433109	SRX8627947	SRS6916252	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92033	0.95428	0.21666	0.2245	0.86571	0.8678	0.74089	0.68247	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60033	60033	SRR12103775	SRX8627946	SRS6916251	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO4 IP	GSM4644245	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	DMSO4 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	GSM4644245	GSM4644245: DMSO4 IP; Danio rerio; RIP Seq	GSM4644245		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644245	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	D4_m6A-IP_S12_R1_001.fastq.gz D4_m6A-IP_S12_R2_001.fastq.gz	fastq fastq	2415539920.0	15891710.0	GSM4644245 r1	0:76 1:76	A:519904759;C:674887600;G:688106098;T:532387711;N:253752	76	76	519904759	674887600	688106098	532387711	253752	SRX8627946	SRS6916251	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.94931	0.94824	0.16515	0.16656	0.74858	0.7497	0.57724	0.58102	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60034	60034	SRR12103774	SRX8627945	SRS6916250	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO3 IP	GSM4644244	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	DMSO3 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	GSM4644244	GSM4644244: DMSO3 IP; Danio rerio; RIP Seq	GSM4644244		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644244	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	D3_m6A-IP_S11_R1_001.fastq.gz D3_m6A-IP_S11_R2_001.fastq.gz	fastq fastq	2419255408.0	15916154.0	GSM4644244 r1	0:76 1:76	A:524637988;C:675158080;G:687344217;T:531861650;N:253473	76	76	524637988	675158080	687344217	531861650	253473	SRX8627945	SRS6916250	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93623	0.93621	0.18212	0.18165	0.74308	0.74426	0.60527	0.60757	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60035	60035	SRR12103773	SRX8627944	SRS6916249	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO2 IP	GSM4644243	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	DMSO2 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	GSM4644243	GSM4644243: DMSO2 IP; Danio rerio; RIP Seq	GSM4644243		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644243	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	D2_m6A-IP_S10_R1_001.fastq.gz D2_m6A-IP_S10_R2_001.fastq.gz	fastq fastq	2698406448.0	17752674.0	GSM4644243 r1	0:76 1:76	A:578126060;C:760791571;G:775423382;T:583783650;N:281785	76	76	578126060	760791571	775423382	583783650	281785	SRX8627944	SRS6916249	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.9433	0.94318	0.17976	0.1816	0.74992	0.75215	0.58844	0.61497	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60036	60036	SRR12103772	SRX8627943	SRS6916248	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO1 IP	GSM4644242	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	DMSO1 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	GSM4644242	GSM4644242: DMSO1 IP; Danio rerio; RIP Seq	GSM4644242		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644242	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	D1_m6A-IP_S9_R1_001.fastq.gz D1_m6A-IP_S9_R2_001.fastq.gz	fastq fastq	2588221344.0	17027772.0	GSM4644242 r1	0:76 1:76	A:552076254;C:730948542;G:744135059;T:560788856;N:272633	76	76	552076254	730948542	744135059	560788856	272633	SRX8627943	SRS6916248	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93871	0.9398	0.17681	0.17588	0.74688	0.74915	0.59376	0.61045	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60037	60037	SRR12103771	SRX8627942	SRS6916247	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO4 Input	GSM4644241	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO4 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644241	GSM4644241: DMSO4 Input; Danio rerio; RIP Seq	GSM4644241		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644241	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	D4_INPUT_S4_R1_001.fastq.gz D4_INPUT_S4_R2_001.fastq.gz	fastq fastq	4085824752.0	26880426.0	GSM4644241 r1	0:76 1:76	A:734095239;C:1307425224;G:1339970208;T:703907493;N:426588	76	76	734095239	1307425224	1339970208	703907493	426588	SRX8627942	SRS6916247	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.94341	0.94693	0.21035	0.21294	0.86306	0.86571	0.66228	0.69648	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60038	60038	SRR12103770	SRX8627941	SRS6916246	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO3 Input	GSM4644240	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO3 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644240	GSM4644240: DMSO3 Input; Danio rerio; RIP Seq	GSM4644240		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644240	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	D3_INPUT_S3_R1_001.fastq.gz D3_INPUT_S3_R2_001.fastq.gz	fastq fastq	3627749800.0	23866775.0	GSM4644240 r1	0:76 1:76	A:677883991;C:1133504965;G:1166401920;T:649582074;N:376850	76	76	677883991	1133504965	1166401920	649582074	376850	SRX8627941	SRS6916246	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92028	0.96282	0.2164	0.22913	0.86517	0.8661	0.73802	0.70578	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60039	60039	SRR12103769	SRX8627940	SRS6916245	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO2 Input	GSM4644239	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO2 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644239	GSM4644239: DMSO2 Input; Danio rerio; RIP Seq	GSM4644239		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644239	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	D2_INPUT_S2_R2_001.fastq.gz D2_INPUT_S2_R1_001.fastq.gz	fastq fastq	2991355592.0	19679971.0	GSM4644239 r1	0:76 1:76	A:555548434;C:937287598;G:965607991;T:532600162;N:311407	76	76	555548434	937287598	965607991	532600162	311407	SRX8627940	SRS6916245	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92966	0.96538	0.21752	0.22835	0.86137	0.86701	0.71065	0.70316	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60040	60040	SRR12103768	SRX8627939	SRS6916244	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO1 Input	GSM4644238	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO1 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644238	GSM4644238: DMSO1 Input; Danio rerio; RIP Seq	GSM4644238		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644238	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097	D1_INPUT_S1_R1_001.fastq.gz D1_INPUT_S1_R2_001.fastq.gz	fastq fastq	3551567552.0	23365576.0	GSM4644238 r1	0:76 1:76	A:659305531;C:1112775748;G:1146213503;T:632894453;N:378317	76	76	659305531	1112775748	1146213503	632894453	378317	SRX8627939	SRS6916244	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92942	0.96366	0.21295	0.2231	0.8574	0.85934	0.75989	0.75855	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;