rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,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.spot_descriptor,experiment.study_ref,run.title,run.attributes,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.r3_length,run.r4_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,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
7950,ERR015567,ERX005930,ERS000089,ERP000263,PRJEB2208,Zebrafish gene three prime end pull down for genome annotation,E-MTAB-308,Transcriptome Analysis,,,,RNA extracted from male adult zebrafish head,,SAMEA708835,SC,ENA FIRST PUBLIC:2010 02 26T10:44:13Z|ENA LAST UPDATE:2018 03 08T15:51:30Z|External Id:SAMEA708835|INSDC center name:SC|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:51:30Z|INSDC status:public|Submitter Id:ZF male head sample1|common name:zebrafish|sample name:ZF male head sample1|scientific name:Danio rerio|sex:male|strain:Tuebingen,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation,E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert,Zebrafish adult male head mRNA three prime end,Zebrafish gene three prime end pull down for genome annotation,20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl.   RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin  magnetic beads.   post washing by pull down on a magnet  the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB.   post further washing  the double strand cDNA was released from the beads with BpmI NEB.   The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.,Experimental Factor: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head|Experimental Factor: SEX:male,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000263,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation,ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16,3444_7.srf,srf,1384012896.0,9105348.0,E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert,0:76 1:76,A:369912216;C:306963547;G:292249178;T:392053840;N:22834115,76,76,,,369912216,306963547,292249178,392053840,22834115,ERX005930,ERS000089,ERA010603,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95932,0.96084,0.20719,0.21321,0.73959,0.74763,0.47227,0.48033,76,76,B,B,biological fallback assumption,illumina,early_illumina,3prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Adult,Adult,Head,Nervous System
70382,SRR19762944,SRX15807635,SRS13499606,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,ZF Ko H5 EW20,GSM6256878,,source name:cpsf6 /  6dpf head|tissue:head|genotype:cpsf6 / |treatment:N1,ZF Ko H5 EW20,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,cpsf6 /  6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:cpsf6 / |treatment:N1,GSM6256878,GSM6256878: ZF Ko H5 EW20; Danio rerio; OTHER,GSM6256878 r1,GSM6256878,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,ZF_Ko_H5_EW20_R1.fastq.gz,fastq,3464837420.0,28635020.0,GSM6256878 r1,0:121,A:1494034798;C:622079032;G:645639126;T:703047177;N:37287,121,,,,1494034798,622079032,645639126,703047177,37287,SRX15807635,SRS13499606,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.47903,,0.15095,,0.82883,,0.6863,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System
70383,SRR19762945,SRX15807634,SRS13499605,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,ZF Ko H4 EW19,GSM6256877,,source name:cpsf6 /  6dpf head|tissue:head|genotype:cpsf6 / |treatment:N1,ZF Ko H4 EW19,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,cpsf6 /  6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:cpsf6 / |treatment:N1,GSM6256877,GSM6256877: ZF Ko H4 EW19; Danio rerio; OTHER,GSM6256877 r1,GSM6256877,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,ZF_Ko_H4_EW19_R1.fastq.gz,fastq,3251893150.0,26875150.0,GSM6256877 r1,0:121,A:1344795862;C:598411565;G:620697978;T:687947810;N:39935,121,,,,1344795862,598411565,620697978,687947810,39935,SRX15807634,SRS13499605,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.50383,,0.16013,,0.82217,,0.6919,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System
70384,SRR19762946,SRX15807633,SRS13499604,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,ZF Ko H3 EW18,GSM6256876,,source name:cpsf6 /  6dpf head|tissue:head|genotype:cpsf6 / |treatment:N1,ZF Ko H3 EW18,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,cpsf6 /  6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:cpsf6 / |treatment:N1,GSM6256876,GSM6256876: ZF Ko H3 EW18; Danio rerio; OTHER,GSM6256876 r1,GSM6256876,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,ZF_Ko_H3_EW18_R1.fastq.gz,fastq,2614428850.0,21606850.0,GSM6256876 r1,0:121,A:1106782184;C:471490720;G:482307751;T:553818128;N:30067,121,,,,1106782184,471490720,482307751,553818128,30067,SRX15807633,SRS13499604,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.49216,,0.17707,,0.824,,0.67519,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System
70385,SRR19762947,SRX15807632,SRS13499603,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,ZF Ko H2 EW17,GSM6256875,,source name:cpsf6 /  6dpf head|tissue:head|genotype:cpsf6 / |treatment:N1,ZF Ko H2 EW17,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,cpsf6 /  6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:cpsf6 / |treatment:N1,GSM6256875,GSM6256875: ZF Ko H2 EW17; Danio rerio; OTHER,GSM6256875 r1,GSM6256875,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,ZF_Ko_H2_EW17_R1.fastq.gz,fastq,2829766984.0,23386504.0,GSM6256875 r1,0:121,A:1154124199;C:523756445;G:540103572;T:611750443;N:32325,121,,,,1154124199,523756445,540103572,611750443,32325,SRX15807632,SRS13499603,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.53128,,0.17359,,0.81479,,0.67717,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System
70386,SRR19762948,SRX15807631,SRS13499602,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,ZF Ko H1 EW16,GSM6256874,,source name:cpsf6 /  6dpf head|tissue:head|genotype:cpsf6 / |treatment:N1,ZF Ko H1 EW16,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,cpsf6 /  6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:cpsf6 / |treatment:N1,GSM6256874,GSM6256874: ZF Ko H1 EW16; Danio rerio; OTHER,GSM6256874 r1,GSM6256874,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,ZF_Ko_H1_EW16_R1.fastq.gz,fastq,3127010139.0,25843059.0,GSM6256874 r1,0:121,A:1303638776;C:565310993;G:598748714;T:659275918;N:35738,121,,,,1303638776,565310993,598748714,659275918,35738,SRX15807631,SRS13499602,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.49184,,0.16601,,0.82201,,0.67657,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System
70387,SRR19762949,SRX15807630,SRS13499601,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,Zf Wt H5 EW15,GSM6256873,,source name:wild type 6dpf head|tissue:head|genotype:wild type|treatment:N1,Zf Wt H5 EW15,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,wild type 6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:wild type|treatment:N1,GSM6256873,GSM6256873: Zf Wt H5 EW15; Danio rerio; OTHER,GSM6256873 r1,GSM6256873,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,Zf_Wt_H5_EW15_R1.fastq.gz,fastq,3020456208.0,24962448.0,GSM6256873 r1,0:121,A:1299290531;C:541614248;G:555748976;T:623766444;N:36009,121,,,,1299290531,541614248,555748976,623766444,36009,SRX15807630,SRS13499601,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.50369,,0.18129,,0.83769,,0.67627,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System
70388,SRR19762950,SRX15807629,SRS13499600,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,Zf Wt H4 EW14,GSM6256872,,source name:wild type 6dpf head|tissue:head|genotype:wild type|treatment:N1,Zf Wt H4 EW14,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,wild type 6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:wild type|treatment:N1,GSM6256872,GSM6256872: Zf Wt H4 EW14; Danio rerio; OTHER,GSM6256872 r1,GSM6256872,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,Zf_Wt_H4_EW14_R1.fastq.gz,fastq,2964716348.0,24501788.0,GSM6256872 r1,0:121,A:1296624390;C:527132924;G:548516138;T:592409475;N:33421,121,,,,1296624390,527132924,548516138,592409475,33421,SRX15807629,SRS13499600,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.46081,,0.15564,,0.85048,,0.6808,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System
70389,SRR19762951,SRX15807628,SRS13499598,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,Zf Wt H3 EW13,GSM6256871,,source name:wild type 6dpf head|tissue:head|genotype:wild type|treatment:N1,Zf Wt H3 EW13,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,wild type 6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:wild type|treatment:N1,GSM6256871,GSM6256871: Zf Wt H3 EW13; Danio rerio; OTHER,GSM6256871 r1,GSM6256871,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,Zf_Wt_H3_EW13_R1.fastq.gz,fastq,3442300565.0,28448765.0,GSM6256871 r1,0:121,A:1485526892;C:608224693;G:650560614;T:697949308;N:39058,121,,,,1485526892,608224693,650560614,697949308,39058,SRX15807628,SRS13499598,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.47353,,0.1692,,0.84898,,0.67905,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System
70390,SRR19762952,SRX15807627,SRS13499599,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,Zf Wt H2 EW12,GSM6256870,,source name:wild type 6dpf head|tissue:head|genotype:wild type|treatment:N1,Zf Wt H2 EW12,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,wild type 6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:wild type|treatment:N1,GSM6256870,GSM6256870: Zf Wt H2 EW12; Danio rerio; OTHER,GSM6256870 r1,GSM6256870,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,Zf_Wt_H2_EW12_R1.fastq.gz,fastq,2948425634.0,24367154.0,GSM6256870 r1,0:121,A:1211451419;C:546445066;G:560022243;T:630468316;N:38590,121,,,,1211451419,546445066,560022243,630468316,38590,SRX15807627,SRS13499599,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.53462,,0.18347,,0.82309,,0.66989,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System
70391,SRR19762953,SRX15807626,SRS13499597,SRP382883,PRJNA851381,Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish],GSE206558,Other,Most pre messenger RNA pre mRNA undergo extensive processing to create distinct transcripts from the same gene. One of these processes  alternative polyadenylation  involves over twenty proteins to bind and cleave the pre mRNA at polyA sites that can lie within the three prime UTR  introns  or exons; this can modulate protein function  but the effect of choosing a site internal to the gene vs. within the three prime UTR remains unclear. Here we show that reduced expression of CPSF6  one of the proteins involved in site selection  derails development in both humans and zebrafish by causing a bidirectional shift in polyA site usage. CPSF6 insufficiency favors the use of intronic polyA sites in neuronal genes  reducing mRNA and protein abundance  but promotes three prime UTR site usage in cardiovascular and skeletal genes  upregulating mRNA and protein.These data thus provides a long sought link between APA and gene expression and shows that polyA site selection influences development.  Overall design: Comparative analysis of alternative polyadenylation using polyA click seq PAC seq on whole larva and head of cpsf6 /  Danio rerio compared to stage matched wt controls.,parent bioproject:PRJNA851372,pubmed:36800428,,Zf Wt H1 EW11,GSM6256869,,source name:wild type 6dpf head|tissue:head|genotype:wild type|treatment:N1,Zf Wt H1 EW11,Raw reads were trimed using fastp Trimed reads were aligned to the reference genome using bowtie2 PCR duplicates were removed using umi tools Samtools were used to sort  convert and index alignment files Deeptools were used to generate bigwig files Assembly: GRCz11 Supplementary files format and content: bigwig files  Library strategy: PAC seq,wild type 6dpf head,,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,tissue:head|genotype:wild type|treatment:N1,GSM6256869,GSM6256869: Zf Wt H1 EW11; Danio rerio; OTHER,GSM6256869 r1,GSM6256869,1,RNA was harvested using Rneasy mini kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. We reverse transcribed 1 ug of total RNA with the partial P7 adapter Illumina 4N 21T and dNTPs with the addition of spiked in azido nucleotides AzVTPs at 5:1. We click ligated the p5 adapter IDT to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with five prime and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200 300 base pairs. We pooled the libraries and sequenced single end  100 base pair reads on a NovaSeq Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP382883,,loader:fastq load.py,Zf_Wt_H1_EW11_R1.fastq.gz,fastq,2689461797.0,22226957.0,GSM6256869 r1,0:121,A:1082451613;C:513056920;G:525960217;T:567960717;N:32330,121,,,,1082451613,513056920,525960217,567960717,32330,SRX15807626,SRS13499597,SRA1440631,Baylor College of Medicine,Baylor College of Medicine,1,0.55368,,0.16655,,0.82828,,0.69871,,121,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2022-06-21,Larval,Larval,Head,Nervous System