metadata: run_metadata: 13 rows where experiment.library_layout = "SINGLE", experiment.library_strategy = "OTHER" and tissue_curation

13 rows where experiment.library_layout = "SINGLE", experiment.library_strategy = "OTHER" and tissue_curation_coarse = "Nervous System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	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.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
43842	43842	SRR6176750	SRX3287416	SRS2596889	SRP120009	PRJNA414416	Simultaneous single cell profiling of lineages and cell types in the vertebrate brain	GSE105010	Other	The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method GESTALT used CRISPR–Cas9 barcode editing for large scale lineage tracing but was restricted to early development and did not identify cell types. Here we present scGESTALT which combines the lineage recording capabilities of GESTALT with cell type identification by single cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points capturing lineage information from later stages of development. Sequencing of 60 000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types brain regions and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease. Overall design: inDrops libraries of single cell transcriptomes and scGESTALT barcodes and genomic DNA GESTALT libraries		pubmed:29608178	ZF3 scGSTLT	GSM2813986	source name:zebrafish brain\|tissue:brain\|developmental stage:23 25dpf	ZF3 scGSTLT	Single cell RNA Sequencing data FASTQ files were processed using the inDrops.py bioinformatics pipeline available at https://github.com/indrops/indrops. Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. Bowtie version1.1.1 was used with parameter –e 200; UMI quantification was used with parameter –u 2 counts were ignored from UMIs split between more than 2 genes. genomic DNA GESTALT and scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 CSV files for transcriptome data were generated using the inDrops pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for genes. Txt files for genomic DNA GESTALT libraries allReadCounts contain lineage barcode sequences HMID column for each cell and their proportion in the sequenced libraries. scGESTALT data GestMaster.txt contains the inDrops cell identifiers CellBarcode and BarcodeKey that were used to match barcodes to transcriptomes. They also contain lineage barcode sequences HMID column for each cell with a corresponding inDrops single cell gene expression profile as well as the the t SNE cluster membership number ClusterIdent column Txt files ending in *stats.txt contain information about the each individually captured UMI or cell per sample. The barcode sequence aligned to a reference unedited sequence mergedRead column mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. inDropsExpMatrix noQ txt file is the gene expression matrix for the full dataset. Columns are individual cells from different batches of whole brains f1 f2 f3 f4 f5 f6 or brain regions fore mid hind . fall.inDrops.Robj is the processed Seurat R object which can be loaded into R and explored.	zebrafish brain	Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	tissue:brain\|developmental stage:23 25dpf	GSM2813986	GSM2813986: ZF3 scGSTLT; Danio rerio; OTHER	GSM2813986		1	Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	GEO Accession:GSM2813986	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq	SRP120009	loader:fastq load.py\|options: appendBCtoName	F6_UMI.merged.fq.gz	fastq	786192951.0	2901081.0	GSM2813986 r1	0:271	A:215364033;C:176865797;G:224444690;T:169518396;N:35	271	215364033	176865797	224444690	169518396	35	SRX3287416	SRS2596889	SRA619743	GEO	Harvard University	1	0.00904	0.0	0.99997	0.0	271	T	under 1.2% mapping rate	illumina	miseq	unknown	other	unknown	sc	single_cell_droplet	indrops	United States	2017-10-16	Larval	Larval	Brain	Nervous System
43843	43843	SRR6176749	SRX3287415	SRS2596888	SRP120009	PRJNA414416	Simultaneous single cell profiling of lineages and cell types in the vertebrate brain	GSE105010	Other	The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method GESTALT used CRISPR–Cas9 barcode editing for large scale lineage tracing but was restricted to early development and did not identify cell types. Here we present scGESTALT which combines the lineage recording capabilities of GESTALT with cell type identification by single cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points capturing lineage information from later stages of development. Sequencing of 60 000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types brain regions and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease. Overall design: inDrops libraries of single cell transcriptomes and scGESTALT barcodes and genomic DNA GESTALT libraries		pubmed:29608178	ZF2 scGSTLT	GSM2813985	source name:zebrafish brain\|tissue:brain\|developmental stage:23 25dpf	ZF2 scGSTLT	Single cell RNA Sequencing data FASTQ files were processed using the inDrops.py bioinformatics pipeline available at https://github.com/indrops/indrops. Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. Bowtie version1.1.1 was used with parameter –e 200; UMI quantification was used with parameter –u 2 counts were ignored from UMIs split between more than 2 genes. genomic DNA GESTALT and scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 CSV files for transcriptome data were generated using the inDrops pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for genes. Txt files for genomic DNA GESTALT libraries allReadCounts contain lineage barcode sequences HMID column for each cell and their proportion in the sequenced libraries. scGESTALT data GestMaster.txt contains the inDrops cell identifiers CellBarcode and BarcodeKey that were used to match barcodes to transcriptomes. They also contain lineage barcode sequences HMID column for each cell with a corresponding inDrops single cell gene expression profile as well as the the t SNE cluster membership number ClusterIdent column Txt files ending in *stats.txt contain information about the each individually captured UMI or cell per sample. The barcode sequence aligned to a reference unedited sequence mergedRead column mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. inDropsExpMatrix noQ txt file is the gene expression matrix for the full dataset. Columns are individual cells from different batches of whole brains f1 f2 f3 f4 f5 f6 or brain regions fore mid hind . fall.inDrops.Robj is the processed Seurat R object which can be loaded into R and explored.	zebrafish brain	Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	tissue:brain\|developmental stage:23 25dpf	GSM2813985	GSM2813985: ZF2 scGSTLT; Danio rerio; OTHER	GSM2813985		1	Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	GEO Accession:GSM2813985	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq	SRP120009	loader:fastq load.py\|options: appendBCtoName	F5_UMI.merged.fq.gz	fastq	106145626.0	391949.0	GSM2813985 r1	0:270.81	A:29282656;C:22944139;G:29276360;T:24642464;N:7	270	29282656	22944139	29276360	24642464	7	SRX3287415	SRS2596888	SRA619743	GEO	Harvard University	1	2e-05	0.0	0.99995	0.0	270	T	under 1.2% mapping rate	illumina	miseq	unknown	other	unknown	sc	single_cell_droplet	indrops	United States	2017-10-16	Larval	Larval	Brain	Nervous System
43844	43844	SRR6176748	SRX3287414	SRS2596887	SRP120009	PRJNA414416	Simultaneous single cell profiling of lineages and cell types in the vertebrate brain	GSE105010	Other	The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method GESTALT used CRISPR–Cas9 barcode editing for large scale lineage tracing but was restricted to early development and did not identify cell types. Here we present scGESTALT which combines the lineage recording capabilities of GESTALT with cell type identification by single cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points capturing lineage information from later stages of development. Sequencing of 60 000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types brain regions and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease. Overall design: inDrops libraries of single cell transcriptomes and scGESTALT barcodes and genomic DNA GESTALT libraries		pubmed:29608178	ZF1 scGSTLT	GSM2813984	source name:zebrafish brain\|tissue:brain\|developmental stage:23 25dpf	ZF1 scGSTLT	Single cell RNA Sequencing data FASTQ files were processed using the inDrops.py bioinformatics pipeline available at https://github.com/indrops/indrops. Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. Bowtie version1.1.1 was used with parameter –e 200; UMI quantification was used with parameter –u 2 counts were ignored from UMIs split between more than 2 genes. genomic DNA GESTALT and scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 CSV files for transcriptome data were generated using the inDrops pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for genes. Txt files for genomic DNA GESTALT libraries allReadCounts contain lineage barcode sequences HMID column for each cell and their proportion in the sequenced libraries. scGESTALT data GestMaster.txt contains the inDrops cell identifiers CellBarcode and BarcodeKey that were used to match barcodes to transcriptomes. They also contain lineage barcode sequences HMID column for each cell with a corresponding inDrops single cell gene expression profile as well as the the t SNE cluster membership number ClusterIdent column Txt files ending in *stats.txt contain information about the each individually captured UMI or cell per sample. The barcode sequence aligned to a reference unedited sequence mergedRead column mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. inDropsExpMatrix noQ txt file is the gene expression matrix for the full dataset. Columns are individual cells from different batches of whole brains f1 f2 f3 f4 f5 f6 or brain regions fore mid hind . fall.inDrops.Robj is the processed Seurat R object which can be loaded into R and explored.	zebrafish brain	Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	tissue:brain\|developmental stage:23 25dpf	GSM2813984	GSM2813984: ZF1 scGSTLT; Danio rerio; OTHER	GSM2813984		1	Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	GEO Accession:GSM2813984	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq	SRP120009	loader:fastq load.py\|options: appendBCtoName	F3_UMI.merged.fq.gz	fastq	817055786.0	3014966.0	GSM2813984 r1	0:271	A:235846657;C:170311176;G:222336783;T:188561170;N:0	271	235846657	170311176	222336783	188561170	0	SRX3287414	SRS2596887	SRA619743	GEO	Harvard University	1	4e-05	0.0	0.99995	0.4	271	T	under 1.2% mapping rate	illumina	miseq	unknown	other	unknown	sc	single_cell_droplet	indrops	United States	2017-10-16	Larval	Larval	Brain	Nervous System
70382	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	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	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	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	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	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	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	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	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	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

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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");;