metadata: run_metadata: 60 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and tissue_curation

60 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "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
75241	75241	SRR26143471	SRX21856058	SRS18582323	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f35	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:35\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f35 Dl	f35 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F42-1_200908_D00404_0493_ACECY3ANXX_TAGGCATG-TATCCTCT_L004_R1_001.fastq.gz 2556F42-2_200908_D00404_0493_ACECY3ANXX_TAGGCATG-TATCCTCT_L005_R1_001.fastq.gz 2556F42-3_200908_D00404_0493_ACECY3ANXX_TAGGCATG-TATCCTCT_L006_R1_001.fastq.gz 2556F42-4_200908_D00404_0493_ACECY3ANXX_TAGGCATG-TATCCTCT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1040429325.0	20400575.0	2556F42 1 200908 D00404 0493 ACECY3ANXX TAGGCATG TATCCTCT L004 R1 001.fastq.gz	0:51	A:259587031;C:255198479;G:241421038;T:284158496;N:64281	51	259587031	255198479	241421038	284158496	64281	SRX21856058	SRS18582323	SRA1717885	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.72615	0.18087	0.79403	0.6392	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-09-22	Adult	Adult	Brain	Nervous System
75242	75242	SRR25609906	SRX21337082	SRS18582315	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f22	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:22\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f22 Dc	f22 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F19-1_200821_D00404_0490_BCECNHANXX_CGATCAGT-GTAAGGAG_L004_R1_001.fastq.gz 2524F19-2_200821_D00404_0490_BCECNHANXX_CGATCAGT-GTAAGGAG_L005_R1_001.fastq.gz 2524F19-3_200821_D00404_0490_BCECNHANXX_CGATCAGT-GTAAGGAG_L006_R1_001.fastq.gz	fastq fastq fastq	1368729075.0	26837825.0	2524F19 1 200821 D00404 0490 BCECNHANXX CGATCAGT GTAAGGAG L004 R1 001.fastq.gz	0:51	A:360325665;C:317884758;G:295959533;T:394421769;N:137350	51	360325665	317884758	295959533	394421769	137350	SRX21337082	SRS18582315	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.69682	0.12734	0.78701	0.67906	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75243	75243	SRR25609907	SRX21337081	SRS18582315	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f22	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:22\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f22 Dm	f22 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F16-1_200821_D00404_0490_BCECNHANXX_CCTAAGAC-TCTCTCCG_L004_R1_001.fastq.gz 2524F16-2_200821_D00404_0490_BCECNHANXX_CCTAAGAC-TCTCTCCG_L005_R1_001.fastq.gz 2524F16-3_200821_D00404_0490_BCECNHANXX_CCTAAGAC-TCTCTCCG_L006_R1_001.fastq.gz	fastq fastq fastq	1390741848.0	27269448.0	2524F16 1 200821 D00404 0490 BCECNHANXX CCTAAGAC TCTCTCCG L004 R1 001.fastq.gz	0:51	A:355778515;C:333350291;G:307305870;T:394167030;N:140142	51	355778515	333350291	307305870	394167030	140142	SRX21337081	SRS18582315	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.68271	0.1658	0.76623	0.58608	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75244	75244	SRR25609908	SRX21337080	SRS18582324	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f21	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:21\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f21 Dl	f21 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F14-1_200821_D00404_0490_BCECNHANXX_CCTAAGAC-CTAAGCCT_L004_R1_001.fastq.gz 2524F14-2_200821_D00404_0490_BCECNHANXX_CCTAAGAC-CTAAGCCT_L005_R1_001.fastq.gz 2524F14-3_200821_D00404_0490_BCECNHANXX_CCTAAGAC-CTAAGCCT_L006_R1_001.fastq.gz	fastq fastq fastq	1438629930.0	28208430.0	2524F14 1 200821 D00404 0490 BCECNHANXX CCTAAGAC CTAAGCCT L004 R1 001.fastq.gz	0:51	A:373059717;C:339824425;G:313418489;T:412183538;N:143761	51	373059717	339824425	313418489	412183538	143761	SRX21337080	SRS18582324	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.67342	0.21574	0.76469	0.6193	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75245	75245	SRR25609909	SRX21337079	SRS18582324	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f21	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:21\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f21 Dp	f21 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F13-1_200821_D00404_0490_BCECNHANXX_CCTAAGAC-AAGGAGTA_L004_R1_001.fastq.gz 2524F13-2_200821_D00404_0490_BCECNHANXX_CCTAAGAC-AAGGAGTA_L005_R1_001.fastq.gz 2524F13-3_200821_D00404_0490_BCECNHANXX_CCTAAGAC-AAGGAGTA_L006_R1_001.fastq.gz	fastq fastq fastq	1366063407.0	26785557.0	2524F13 1 200821 D00404 0490 BCECNHANXX CCTAAGAC AAGGAGTA L004 R1 001.fastq.gz	0:51	A:362178882;C:314094030;G:296755145;T:392898841;N:136509	51	362178882	314094030	296755145	392898841	136509	SRX21337079	SRS18582324	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.72509	0.19957	0.75306	0.62708	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75246	75246	SRR25609910	SRX21337078	SRS18582324	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f21	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:21\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f21 Dc	f21 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F12-1_200821_D00404_0490_BCECNHANXX_CCTAAGAC-ACTGCATA_L004_R1_001.fastq.gz 2524F12-2_200821_D00404_0490_BCECNHANXX_CCTAAGAC-ACTGCATA_L005_R1_001.fastq.gz 2524F12-3_200821_D00404_0490_BCECNHANXX_CCTAAGAC-ACTGCATA_L006_R1_001.fastq.gz	fastq fastq fastq	1408047729.0	27608779.0	2524F12 1 200821 D00404 0490 BCECNHANXX CCTAAGAC ACTGCATA L004 R1 001.fastq.gz	0:51	A:380296480;C:316922224;G:298608551;T:412080509;N:139965	51	380296480	316922224	298608551	412080509	139965	SRX21337078	SRS18582324	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.71903	0.16215	0.78064	0.70757	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75247	75247	SRR25609911	SRX21337077	SRS18582325	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f36	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:36\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f36 Dl	f36 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F49-4_200908_D00404_0493_ACECY3ANXX_CTCTCTAC-CTCTCTAT_L007_R1_001.fastq.gz 2556F49-3_200908_D00404_0493_ACECY3ANXX_CTCTCTAC-CTCTCTAT_L006_R1_001.fastq.gz 2556F49-2_200908_D00404_0493_ACECY3ANXX_CTCTCTAC-CTCTCTAT_L005_R1_001.fastq.gz 2556F49-1_200908_D00404_0493_ACECY3ANXX_CTCTCTAC-CTCTCTAT_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1055166999.0	20689549.0	2556F49 1 200908 D00404 0493 ACECY3ANXX CTCTCTAC CTCTCTAT L004 R1 001.fastq.gz	0:51	A:263524082;C:258526225;G:242273601;T:290778510;N:64581	51	263524082	258526225	242273601	290778510	64581	SRX21337077	SRS18582325	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.72298	0.17009	0.75418	0.53899	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75248	75248	SRR25609912	SRX21337076	SRS18582325	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f36	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:36\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f36 Dp	f36 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F48-1_200908_D00404_0493_ACECY3ANXX_TAGGCATG-TCTCTCCG_L004_R1_001.fastq.gz 2556F48-2_200908_D00404_0493_ACECY3ANXX_TAGGCATG-TCTCTCCG_L005_R1_001.fastq.gz 2556F48-3_200908_D00404_0493_ACECY3ANXX_TAGGCATG-TCTCTCCG_L006_R1_001.fastq.gz 2556F48-4_200908_D00404_0493_ACECY3ANXX_TAGGCATG-TCTCTCCG_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1187440140.0	23283140.0	2556F48 1 200908 D00404 0493 ACECY3ANXX TAGGCATG TCTCTCCG L004 R1 001.fastq.gz	0:51	A:300590991;C:286990173;G:269833876;T:329952311;N:72789	51	300590991	286990173	269833876	329952311	72789	SRX21337076	SRS18582325	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.72191	0.18451	0.7708	0.59459	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75249	75249	SRR25609913	SRX21337075	SRS18582325	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f36	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:36\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f36 Dc	f36 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F47-1_200908_D00404_0493_ACECY3ANXX_TAGGCATG-CGTCTAAT_L004_R1_001.fastq.gz 2556F47-2_200908_D00404_0493_ACECY3ANXX_TAGGCATG-CGTCTAAT_L005_R1_001.fastq.gz 2556F47-3_200908_D00404_0493_ACECY3ANXX_TAGGCATG-CGTCTAAT_L006_R1_001.fastq.gz 2556F47-4_200908_D00404_0493_ACECY3ANXX_TAGGCATG-CGTCTAAT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1056839034.0	20722334.0	2556F47 1 200908 D00404 0493 ACECY3ANXX TAGGCATG CGTCTAAT L004 R1 001.fastq.gz	0:51	A:273921750;C:250420125;G:235612441;T:296820106;N:64612	51	273921750	250420125	235612441	296820106	64612	SRX21337075	SRS18582325	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.73416	0.17257	0.77638	0.57796	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75250	75250	SRR25609914	SRX21337074	SRS18582325	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f36	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:36\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f36 Dm	f36 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F44-1_200908_D00404_0493_ACECY3ANXX_TAGGCATG-ACTGCATA_L004_R1_001.fastq.gz 2556F44-2_200908_D00404_0493_ACECY3ANXX_TAGGCATG-ACTGCATA_L005_R1_001.fastq.gz 2556F44-3_200908_D00404_0493_ACECY3ANXX_TAGGCATG-ACTGCATA_L006_R1_001.fastq.gz 2556F44-4_200908_D00404_0493_ACECY3ANXX_TAGGCATG-ACTGCATA_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1073973453.0	21058303.0	2556F44 1 200908 D00404 0493 ACECY3ANXX TAGGCATG ACTGCATA L004 R1 001.fastq.gz	0:51	A:267145001;C:264800059;G:245237465;T:296725601;N:65327	51	267145001	264800059	245237465	296725601	65327	SRX21337074	SRS18582325	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.69877	0.1658	0.74255	0.53459	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75251	75251	SRR25609915	SRX21337073	SRS18582323	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f35	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:35\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f35 Dp	f35 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F41-1_200908_D00404_0493_ACECY3ANXX_TAGGCATG-CTCTCTAT_L004_R1_001.fastq.gz 2556F41-2_200908_D00404_0493_ACECY3ANXX_TAGGCATG-CTCTCTAT_L005_R1_001.fastq.gz 2556F41-3_200908_D00404_0493_ACECY3ANXX_TAGGCATG-CTCTCTAT_L006_R1_001.fastq.gz 2556F41-4_200908_D00404_0493_ACECY3ANXX_TAGGCATG-CTCTCTAT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1155296676.0	22652876.0	2556F41 1 200908 D00404 0493 ACECY3ANXX TAGGCATG CTCTCTAT L004 R1 001.fastq.gz	0:51	A:305708591;C:266923781;G:255185465;T:327408621;N:70218	51	305708591	266923781	255185465	327408621	70218	SRX21337073	SRS18582323	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.76807	0.20478	0.74334	0.57745	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75252	75252	SRR25609916	SRX21337072	SRS18582323	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f35	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:35\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f35 Dc	f35 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F40-1_200908_D00404_0493_ACECY3ANXX_GGACTCCT-TCTCTCCG_L004_R1_001.fastq.gz 2556F40-2_200908_D00404_0493_ACECY3ANXX_GGACTCCT-TCTCTCCG_L005_R1_001.fastq.gz 2556F40-3_200908_D00404_0493_ACECY3ANXX_GGACTCCT-TCTCTCCG_L006_R1_001.fastq.gz 2556F40-4_200908_D00404_0493_ACECY3ANXX_GGACTCCT-TCTCTCCG_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1217738016.0	23877216.0	2556F40 1 200908 D00404 0493 ACECY3ANXX GGACTCCT TCTCTCCG L004 R1 001.fastq.gz	0:51	A:311937058;C:291873810;G:274741578;T:339111280;N:74290	51	311937058	291873810	274741578	339111280	74290	SRX21337072	SRS18582323	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.74112	0.15129	0.75935	0.60254	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75253	75253	SRR25609917	SRX21337071	SRS18582324	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f21	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:21\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f21 Dm	f21 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F9-1_200821_D00404_0490_BCECNHANXX_CCTAAGAC-CTCTCTAT_L004_R1_001.fastq.gz 2524F9-2_200821_D00404_0490_BCECNHANXX_CCTAAGAC-CTCTCTAT_L005_R1_001.fastq.gz 2524F9-3_200821_D00404_0490_BCECNHANXX_CCTAAGAC-CTCTCTAT_L006_R1_001.fastq.gz	fastq fastq fastq	1383698901.0	27131351.0	2524F9 1 200821 D00404 0490 BCECNHANXX CCTAAGAC CTCTCTAT L004 R1 001.fastq.gz	0:51	A:369743407;C:315577107;G:297040256;T:401198028;N:140103	51	369743407	315577107	297040256	401198028	140103	SRX21337071	SRS18582324	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.71583	0.27236	0.75485	0.5799	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75254	75254	SRR25609918	SRX21337070	SRS18582323	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f35	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:35\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f35 Dm	f35 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F37-1_200908_D00404_0493_ACECY3ANXX_GGACTCCT-AAGGAGTA_L004_R1_001.fastq.gz 2556F37-2_200908_D00404_0493_ACECY3ANXX_GGACTCCT-AAGGAGTA_L005_R1_001.fastq.gz 2556F37-3_200908_D00404_0493_ACECY3ANXX_GGACTCCT-AAGGAGTA_L006_R1_001.fastq.gz 2556F37-4_200908_D00404_0493_ACECY3ANXX_GGACTCCT-AAGGAGTA_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1317149460.0	25826460.0	2556F37 1 200908 D00404 0493 ACECY3ANXX GGACTCCT AAGGAGTA L004 R1 001.fastq.gz	0:51	A:343226479;C:309959829;G:294460178;T:369422401;N:80573	51	343226479	309959829	294460178	369422401	80573	SRX21337070	SRS18582323	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.7526	0.21197	0.74454	0.54896	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75255	75255	SRR25609919	SRX21337069	SRS18582322	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f34	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:34\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f34 Dl	f34 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F35-1_200908_D00404_0493_ACECY3ANXX_GGACTCCT-GTAAGGAG_L004_R1_001.fastq.gz 2556F35-2_200908_D00404_0493_ACECY3ANXX_GGACTCCT-GTAAGGAG_L005_R1_001.fastq.gz 2556F35-3_200908_D00404_0493_ACECY3ANXX_GGACTCCT-GTAAGGAG_L006_R1_001.fastq.gz 2556F35-4_200908_D00404_0493_ACECY3ANXX_GGACTCCT-GTAAGGAG_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1101392430.0	21595930.0	2556F35 1 200908 D00404 0493 ACECY3ANXX GGACTCCT GTAAGGAG L004 R1 001.fastq.gz	0:51	A:270416566;C:275928451;G:256480404;T:298498966;N:68043	51	270416566	275928451	256480404	298498966	68043	SRX21337069	SRS18582322	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.70387	0.16319	0.7668	0.57622	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75256	75256	SRR25609920	SRX21337068	SRS18582322	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f34	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:34\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f34 Dp	f34 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F34-1_200908_D00404_0493_ACECY3ANXX_GGACTCCT-TATCCTCT_L004_R1_001.fastq.gz 2556F34-2_200908_D00404_0493_ACECY3ANXX_GGACTCCT-TATCCTCT_L005_R1_001.fastq.gz 2556F34-3_200908_D00404_0493_ACECY3ANXX_GGACTCCT-TATCCTCT_L006_R1_001.fastq.gz 2556F34-4_200908_D00404_0493_ACECY3ANXX_GGACTCCT-TATCCTCT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1115056350.0	21863850.0	2556F34 1 200908 D00404 0493 ACECY3ANXX GGACTCCT TATCCTCT L004 R1 001.fastq.gz	0:51	A:273769207;C:279307082;G:259988688;T:301923307;N:68066	51	273769207	279307082	259988688	301923307	68066	SRX21337068	SRS18582322	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.71328	0.16362	0.77305	0.60138	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75257	75257	SRR25609921	SRX21337067	SRS18582322	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f34	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:34\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f34 Dc	f34 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F33-1_200908_D00404_0493_ACECY3ANXX_GGACTCCT-CTCTCTAT_L004_R1_001.fastq.gz 2556F33-2_200908_D00404_0493_ACECY3ANXX_GGACTCCT-CTCTCTAT_L005_R1_001.fastq.gz 2556F33-3_200908_D00404_0493_ACECY3ANXX_GGACTCCT-CTCTCTAT_L006_R1_001.fastq.gz 2556F33-4_200908_D00404_0493_ACECY3ANXX_GGACTCCT-CTCTCTAT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1265440917.0	24812567.0	2556F33 1 200908 D00404 0493 ACECY3ANXX GGACTCCT CTCTCTAT L004 R1 001.fastq.gz	0:51	A:332463888;C:294728187;G:281678767;T:356490805;N:79270	51	332463888	294728187	281678767	356490805	79270	SRX21337067	SRS18582322	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.76652	0.17639	0.75645	0.61581	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75258	75258	SRR25609922	SRX21337066	SRS18582322	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f34	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:34\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f34 Dm	f34 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F30-1_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-CTAAGCCT_L004_R1_001.fastq.gz 2556F30-2_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-CTAAGCCT_L005_R1_001.fastq.gz 2556F30-3_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-CTAAGCCT_L006_R1_001.fastq.gz 2556F30-4_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-CTAAGCCT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1299731532.0	25484932.0	2556F30 1 200908 D00404 0493 ACECY3ANXX TCCTGAGC CTAAGCCT L004 R1 001.fastq.gz	0:51	A:331824329;C:312293000;G:291737763;T:363797530;N:78910	51	331824329	312293000	291737763	363797530	78910	SRX21337066	SRS18582322	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.71649	0.17761	0.73235	0.55221	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75259	75259	SRR25609923	SRX21337065	SRS18582321	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f33	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:33\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f33 Dp	f33 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F27-1_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-GTAAGGAG_L004_R1_001.fastq.gz 2556F27-2_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-GTAAGGAG_L005_R1_001.fastq.gz 2556F27-3_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-GTAAGGAG_L006_R1_001.fastq.gz 2556F27-4_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-GTAAGGAG_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1191919215.0	23370965.0	2556F27 1 200908 D00404 0493 ACECY3ANXX TCCTGAGC GTAAGGAG L004 R1 001.fastq.gz	0:51	A:316991438;C:273983938;G:261204926;T:339665710;N:73203	51	316991438	273983938	261204926	339665710	73203	SRX21337065	SRS18582321	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.7688	0.20313	0.73825	0.56206	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75260	75260	SRR25609924	SRX21337064	SRS18582321	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f33	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:33\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f33 Dc	f33 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F26-1_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-TATCCTCT_L004_R1_001.fastq.gz 2556F26-2_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-TATCCTCT_L005_R1_001.fastq.gz 2556F26-3_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-TATCCTCT_L006_R1_001.fastq.gz 2556F26-4_200908_D00404_0493_ACECY3ANXX_TCCTGAGC-TATCCTCT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1188852942.0	23310842.0	2556F26 1 200908 D00404 0493 ACECY3ANXX TCCTGAGC TATCCTCT L004 R1 001.fastq.gz	0:51	A:299022929;C:289871050;G:268968275;T:330917526;N:73162	51	299022929	289871050	268968275	330917526	73162	SRX21337064	SRS18582321	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.70669	0.13246	0.76079	0.60593	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75261	75261	SRR25609925	SRX21337063	SRS18582321	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f33	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:33\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f33 Dm	f33 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F23-1_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-CGTCTAAT_L004_R1_001.fastq.gz 2556F23-2_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-CGTCTAAT_L005_R1_001.fastq.gz 2556F23-3_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-CGTCTAAT_L006_R1_001.fastq.gz 2556F23-4_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-CGTCTAAT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1166658711.0	22875661.0	2556F23 1 200908 D00404 0493 ACECY3ANXX AGGCAGAA CGTCTAAT L004 R1 001.fastq.gz	0:51	A:289696778;C:288748081;G:266467277;T:321675641;N:70934	51	289696778	288748081	266467277	321675641	70934	SRX21337063	SRS18582321	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.69386	0.15766	0.74239	0.53207	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75262	75262	SRR25609926	SRX21337062	SRS18582320	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f32	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:32\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f32 Dl	f32 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F21-1_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-AAGGAGTA_L004_R1_001.fastq.gz 2556F21-2_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-AAGGAGTA_L005_R1_001.fastq.gz 2556F21-3_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-AAGGAGTA_L006_R1_001.fastq.gz 2556F21-4_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-AAGGAGTA_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1213725693.0	23798543.0	2556F21 1 200908 D00404 0493 ACECY3ANXX AGGCAGAA AAGGAGTA L004 R1 001.fastq.gz	0:51	A:310132207;C:291776453;G:273787346;T:337954066;N:75621	51	310132207	291776453	273787346	337954066	75621	SRX21337062	SRS18582320	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.73268	0.18782	0.73722	0.54739	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75263	75263	SRR25609927	SRX21337061	SRS18582320	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f32	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:32\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f32 Dp	f32 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F20-1_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-ACTGCATA_L004_R1_001.fastq.gz 2556F20-2_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-ACTGCATA_L005_R1_001.fastq.gz 2556F20-3_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-ACTGCATA_L006_R1_001.fastq.gz 2556F20-4_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-ACTGCATA_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1072803768.0	21035368.0	2556F20 1 200908 D00404 0493 ACECY3ANXX AGGCAGAA ACTGCATA L004 R1 001.fastq.gz	0:51	A:268037522;C:263421638;G:244415486;T:296862785;N:66337	51	268037522	263421638	244415486	296862785	66337	SRX21337061	SRS18582320	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.70554	0.17272	0.7415	0.54408	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75264	75264	SRR25609928	SRX21337060	SRS18582314	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f20	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:20\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f20 Dl	f20 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F7-1_200821_D00404_0490_BCECNHANXX_ACTGAGCG-CGTCTAAT_L004_R1_001.fastq.gz 2524F7-2_200821_D00404_0490_BCECNHANXX_ACTGAGCG-CGTCTAAT_L005_R1_001.fastq.gz 2524F7-3_200821_D00404_0490_BCECNHANXX_ACTGAGCG-CGTCTAAT_L006_R1_001.fastq.gz	fastq fastq fastq	1026815793.0	20133643.0	2524F7 1 200821 D00404 0490 BCECNHANXX ACTGAGCG CGTCTAAT L004 R1 001.fastq.gz	0:51	A:260601262;C:248517077;G:227743539;T:289861765;N:92150	51	260601262	248517077	227743539	289861765	92150	SRX21337060	SRS18582314	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.66007	0.18828	0.76518	0.59914	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75265	75265	SRR25609929	SRX21337059	SRS18582320	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f32	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:32\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f32 Dc	f32 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F19-1_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-GTAAGGAG_L004_R1_001.fastq.gz 2556F19-2_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-GTAAGGAG_L005_R1_001.fastq.gz 2556F19-3_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-GTAAGGAG_L006_R1_001.fastq.gz 2556F19-4_200908_D00404_0493_ACECY3ANXX_AGGCAGAA-GTAAGGAG_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1252180101.0	24552551.0	2556F19 1 200908 D00404 0493 ACECY3ANXX AGGCAGAA GTAAGGAG L004 R1 001.fastq.gz	0:51	A:323343132;C:298020101;G:281347786;T:349391791;N:77291	51	323343132	298020101	281347786	349391791	77291	SRX21337059	SRS18582320	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.74924	0.16347	0.75517	0.61323	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75266	75266	SRR25609930	SRX21337058	SRS18582320	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f32	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:32\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f32 Dm	f32 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F16-1_200908_D00404_0493_ACECY3ANXX_CGTACTAG-TCTCTCCG_L004_R1_001.fastq.gz 2556F16-2_200908_D00404_0493_ACECY3ANXX_CGTACTAG-TCTCTCCG_L005_R1_001.fastq.gz 2556F16-3_200908_D00404_0493_ACECY3ANXX_CGTACTAG-TCTCTCCG_L006_R1_001.fastq.gz 2556F16-4_200908_D00404_0493_ACECY3ANXX_CGTACTAG-TCTCTCCG_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1228702965.0	24092215.0	2556F16 1 200908 D00404 0493 ACECY3ANXX CGTACTAG TCTCTCCG L004 R1 001.fastq.gz	0:51	A:322048989;C:286945823;G:270094494;T:349537500;N:76159	51	322048989	286945823	270094494	349537500	76159	SRX21337058	SRS18582320	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.73366	0.20938	0.74923	0.55506	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75267	75267	SRR25609931	SRX21337057	SRS18582319	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f31	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:31\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f31 Dl	f31 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F14-1_200908_D00404_0493_ACECY3ANXX_CGTACTAG-CTAAGCCT_L004_R1_001.fastq.gz 2556F14-2_200908_D00404_0493_ACECY3ANXX_CGTACTAG-CTAAGCCT_L005_R1_001.fastq.gz 2556F14-3_200908_D00404_0493_ACECY3ANXX_CGTACTAG-CTAAGCCT_L006_R1_001.fastq.gz 2556F14-4_200908_D00404_0493_ACECY3ANXX_CGTACTAG-CTAAGCCT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1029444792.0	20185192.0	2556F14 1 200908 D00404 0493 ACECY3ANXX CGTACTAG CTAAGCCT L004 R1 001.fastq.gz	0:51	A:264924143;C:245801046;G:232641783;T:286017298;N:60522	51	264924143	245801046	232641783	286017298	60522	SRX21337057	SRS18582319	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.71324	0.21005	0.76654	0.57247	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75268	75268	SRR25609932	SRX21337056	SRS18582319	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f31	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:31\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f31 Dp	f31 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F13-1_200908_D00404_0493_ACECY3ANXX_CGTACTAG-AAGGAGTA_L004_R1_001.fastq.gz 2556F13-2_200908_D00404_0493_ACECY3ANXX_CGTACTAG-AAGGAGTA_L005_R1_001.fastq.gz 2556F13-3_200908_D00404_0493_ACECY3ANXX_CGTACTAG-AAGGAGTA_L006_R1_001.fastq.gz 2556F13-4_200908_D00404_0493_ACECY3ANXX_CGTACTAG-AAGGAGTA_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1183833777.0	23212427.0	2556F13 1 200908 D00404 0493 ACECY3ANXX CGTACTAG AAGGAGTA L004 R1 001.fastq.gz	0:51	A:312792177;C:274201924;G:263027486;T:333739944;N:72246	51	312792177	274201924	263027486	333739944	72246	SRX21337056	SRS18582319	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.77872	0.2141	0.74905	0.56662	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75269	75269	SRR25609933	SRX21337055	SRS18582319	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f31	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:31\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f31 Dc	f31 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F12-1_200908_D00404_0493_ACECY3ANXX_CGTACTAG-ACTGCATA_L004_R1_001.fastq.gz 2556F12-2_200908_D00404_0493_ACECY3ANXX_CGTACTAG-ACTGCATA_L005_R1_001.fastq.gz 2556F12-3_200908_D00404_0493_ACECY3ANXX_CGTACTAG-ACTGCATA_L006_R1_001.fastq.gz 2556F12-4_200908_D00404_0493_ACECY3ANXX_CGTACTAG-ACTGCATA_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1143161022.0	22414922.0	2556F12 1 200908 D00404 0493 ACECY3ANXX CGTACTAG ACTGCATA L004 R1 001.fastq.gz	0:51	A:295139379;C:271535804;G:258007124;T:318407781;N:70934	51	295139379	271535804	258007124	318407781	70934	SRX21337055	SRS18582319	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.75103	0.17265	0.77169	0.50242	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75270	75270	SRR25609934	SRX21337054	SRS18582319	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f31	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:31\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f31 Dm	f31 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F9-1_200908_D00404_0493_ACECY3ANXX_CGTACTAG-CTCTCTAT_L004_R1_001.fastq.gz 2556F9-2_200908_D00404_0493_ACECY3ANXX_CGTACTAG-CTCTCTAT_L005_R1_001.fastq.gz 2556F9-3_200908_D00404_0493_ACECY3ANXX_CGTACTAG-CTCTCTAT_L006_R1_001.fastq.gz 2556F9-4_200908_D00404_0493_ACECY3ANXX_CGTACTAG-CTCTCTAT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1191978630.0	23372130.0	2556F9 1 200908 D00404 0493 ACECY3ANXX CGTACTAG CTCTCTAT L004 R1 001.fastq.gz	0:51	A:311856874;C:278677077;G:266115474;T:335256862;N:72343	51	311856874	278677077	266115474	335256862	72343	SRX21337054	SRS18582319	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.76588	0.20741	0.74347	0.50222	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75271	75271	SRR25609935	SRX21337053	SRS18582318	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f30	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:30\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f30 Dl	f30 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F7-4_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-CGTCTAAT_L007_R1_001.fastq.gz 2556F7-3_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-CGTCTAAT_L006_R1_001.fastq.gz 2556F7-2_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-CGTCTAAT_L005_R1_001.fastq.gz 2556F7-1_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-CGTCTAAT_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1167263010.0	22887510.0	2556F7 1 200908 D00404 0493 ACECY3ANXX TAAGGCGA CGTCTAAT L004 R1 001.fastq.gz	0:51	A:309051299;C:269678911;G:255300774;T:333160957;N:71069	51	309051299	269678911	255300774	333160957	71069	SRX21337053	SRS18582318	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.74671	0.23651	0.7345	0.55689	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75272	75272	SRR25609936	SRX21337052	SRS18582318	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f30	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:30\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f30 Dp	f30 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F6-1_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-CTAAGCCT_L004_R1_001.fastq.gz 2556F6-2_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-CTAAGCCT_L005_R1_001.fastq.gz 2556F6-3_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-CTAAGCCT_L006_R1_001.fastq.gz 2556F6-4_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-CTAAGCCT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	730790985.0	14329235.0	2556F6 1 200908 D00404 0493 ACECY3ANXX TAAGGCGA CTAAGCCT L004 R1 001.fastq.gz	0:51	A:191033739;C:172134643;G:162119469;T:205460903;N:42231	51	191033739	172134643	162119469	205460903	42231	SRX21337052	SRS18582318	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.72822	0.22363	0.7683	0.54751	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75273	75273	SRR25609937	SRX21337051	SRS18582318	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f30	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:30\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f30 Dc	f30 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F5-1_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-AAGGAGTA_L004_R1_001.fastq.gz 2556F5-2_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-AAGGAGTA_L005_R1_001.fastq.gz 2556F5-3_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-AAGGAGTA_L006_R1_001.fastq.gz 2556F5-4_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-AAGGAGTA_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1241901561.0	24351011.0	2556F5 1 200908 D00404 0493 ACECY3ANXX TAAGGCGA AAGGAGTA L004 R1 001.fastq.gz	0:51	A:326238443;C:288886966;G:274508143;T:352191293;N:76716	51	326238443	288886966	274508143	352191293	76716	SRX21337051	SRS18582318	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.72948	0.21168	0.76075	0.5195	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75274	75274	SRR25609938	SRX21337050	SRS18582318	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f30	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:30\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f30 Dm	f30 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2556F2-1_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-TATCCTCT_L004_R1_001.fastq.gz 2556F2-2_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-TATCCTCT_L005_R1_001.fastq.gz 2556F2-3_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-TATCCTCT_L006_R1_001.fastq.gz 2556F2-4_200908_D00404_0493_ACECY3ANXX_TAAGGCGA-TATCCTCT_L007_R1_001.fastq.gz	fastq fastq fastq fastq	1156225284.0	22671084.0	2556F2 1 200908 D00404 0493 ACECY3ANXX TAAGGCGA TATCCTCT L004 R1 001.fastq.gz	0:51	A:310810127;C:261969062;G:247481781;T:335891118;N:73196	51	310810127	261969062	247481781	335891118	73196	SRX21337050	SRS18582318	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.73161	0.25224	0.74617	0.54265	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75275	75275	SRR25609939	SRX21337049	SRS18582314	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f20	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:20\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f20 Dp	f20 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F6-3_200821_D00404_0490_BCECNHANXX_ACTCGCTA-CTAAGCCT_L006_R1_001.fastq.gz 2524F6-2_200821_D00404_0490_BCECNHANXX_ACTCGCTA-CTAAGCCT_L005_R1_001.fastq.gz 2524F6-1_200821_D00404_0490_BCECNHANXX_ACTCGCTA-CTAAGCCT_L004_R1_001.fastq.gz	fastq fastq fastq	1345965786.0	26391486.0	2524F6 1 200821 D00404 0490 BCECNHANXX ACTCGCTA CTAAGCCT L004 R1 001.fastq.gz	0:51	A:351448846;C:315636670;G:296052222;T:382693173;N:134875	51	351448846	315636670	296052222	382693173	134875	SRX21337049	SRS18582314	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.72109	0.17887	0.75552	0.61186	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75276	75276	SRR25609940	SRX21337048	SRS18582317	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f24	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:24\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f24 Dl	f24 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F35-1_200821_D00404_0490_BCECNHANXX_TCGACGTC-GTAAGGAG_L004_R1_001.fastq.gz 2524F35-2_200821_D00404_0490_BCECNHANXX_TCGACGTC-GTAAGGAG_L005_R1_001.fastq.gz 2524F35-3_200821_D00404_0490_BCECNHANXX_TCGACGTC-GTAAGGAG_L006_R1_001.fastq.gz	fastq fastq fastq	1299505296.0	25480496.0	2524F35 1 200821 D00404 0490 BCECNHANXX TCGACGTC GTAAGGAG L004 R1 001.fastq.gz	0:51	A:334254701;C:310229900;G:284636696;T:370252708;N:131291	51	334254701	310229900	284636696	370252708	131291	SRX21337048	SRS18582317	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.67172	0.18414	0.75948	0.59378	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75277	75277	SRR25609941	SRX21337047	SRS18582317	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f24	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:24\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f24 Dp	f24 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F34-1_200821_D00404_0490_BCECNHANXX_TCGACGTC-TATCCTCT_L004_R1_001.fastq.gz 2524F34-2_200821_D00404_0490_BCECNHANXX_TCGACGTC-TATCCTCT_L005_R1_001.fastq.gz 2524F34-3_200821_D00404_0490_BCECNHANXX_TCGACGTC-TATCCTCT_L006_R1_001.fastq.gz	fastq fastq fastq	1425394716.0	27948916.0	2524F34 1 200821 D00404 0490 BCECNHANXX TCGACGTC TATCCTCT L004 R1 001.fastq.gz	0:51	A:361837350;C:344282267;G:312480811;T:406651814;N:142474	51	361837350	344282267	312480811	406651814	142474	SRX21337047	SRS18582317	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.64429	0.17561	0.75438	0.55915	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75278	75278	SRR25609942	SRX21337046	SRS18582317	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f24	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:24\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f24 Dc	f24 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F33-1_200821_D00404_0490_BCECNHANXX_TCGACGTC-CTCTCTAT_L004_R1_001.fastq.gz 2524F33-2_200821_D00404_0490_BCECNHANXX_TCGACGTC-CTCTCTAT_L005_R1_001.fastq.gz 2524F33-3_200821_D00404_0490_BCECNHANXX_TCGACGTC-CTCTCTAT_L006_R1_001.fastq.gz	fastq fastq fastq	1326762552.0	26014952.0	2524F33 1 200821 D00404 0490 BCECNHANXX TCGACGTC CTCTCTAT L004 R1 001.fastq.gz	0:51	A:340637915;C:317128153;G:291366840;T:377494272;N:135372	51	340637915	317128153	291366840	377494272	135372	SRX21337046	SRS18582317	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.67552	0.14592	0.78196	0.67118	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75279	75279	SRR25609943	SRX21337045	SRS18582317	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f24	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:24\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f24 Dm	f24 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F30-1_200821_D00404_0490_BCECNHANXX_TGCAGCTA-CTAAGCCT_L004_R1_001.fastq.gz 2524F30-2_200821_D00404_0490_BCECNHANXX_TGCAGCTA-CTAAGCCT_L005_R1_001.fastq.gz 2524F30-3_200821_D00404_0490_BCECNHANXX_TGCAGCTA-CTAAGCCT_L006_R1_001.fastq.gz	fastq fastq fastq	1300641525.0	25502775.0	2524F30 1 200821 D00404 0490 BCECNHANXX TGCAGCTA CTAAGCCT L004 R1 001.fastq.gz	0:51	A:337878510;C:306753836;G:284047898;T:371833121;N:128160	51	337878510	306753836	284047898	371833121	128160	SRX21337045	SRS18582317	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.68639	0.19082	0.75582	0.59655	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75280	75280	SRR25609944	SRX21337044	SRS18582316	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f23	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:23\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f23 Dl	f23 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F28-1_200821_D00404_0490_BCECNHANXX_TGCAGCTA-ACTGCATA_L004_R1_001.fastq.gz 2524F28-2_200821_D00404_0490_BCECNHANXX_TGCAGCTA-ACTGCATA_L005_R1_001.fastq.gz 2524F28-3_200821_D00404_0490_BCECNHANXX_TGCAGCTA-ACTGCATA_L006_R1_001.fastq.gz	fastq fastq fastq	657791472.0	12897872.0	2524F28 1 200821 D00404 0490 BCECNHANXX TGCAGCTA ACTGCATA L004 R1 001.fastq.gz	0:51	A:167368979;C:158769356;G:150895386;T:180703633;N:54118	51	167368979	158769356	150895386	180703633	54118	SRX21337044	SRS18582316	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.75209	0.15722	0.78476	0.56215	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75281	75281	SRR25609945	SRX21337043	SRS18582316	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f23	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:23\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f23 Dp	f23 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F27-1_200821_D00404_0490_BCECNHANXX_TGCAGCTA-GTAAGGAG_L004_R1_001.fastq.gz 2524F27-2_200821_D00404_0490_BCECNHANXX_TGCAGCTA-GTAAGGAG_L005_R1_001.fastq.gz 2524F27-3_200821_D00404_0490_BCECNHANXX_TGCAGCTA-GTAAGGAG_L006_R1_001.fastq.gz	fastq fastq fastq	1331124837.0	26100487.0	2524F27 1 200821 D00404 0490 BCECNHANXX TGCAGCTA GTAAGGAG L004 R1 001.fastq.gz	0:51	A:343365280;C:316530308;G:292327065;T:378768714;N:133470	51	343365280	316530308	292327065	378768714	133470	SRX21337043	SRS18582316	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.68947	0.19801	0.75243	0.58902	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75282	75282	SRR25609946	SRX21337042	SRS18582316	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f23	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:23\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f23 Dc	f23 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F26-1_200821_D00404_0490_BCECNHANXX_TGCAGCTA-TATCCTCT_L004_R1_001.fastq.gz 2524F26-2_200821_D00404_0490_BCECNHANXX_TGCAGCTA-TATCCTCT_L005_R1_001.fastq.gz 2524F26-3_200821_D00404_0490_BCECNHANXX_TGCAGCTA-TATCCTCT_L006_R1_001.fastq.gz	fastq fastq fastq	1357438593.0	26616443.0	2524F26 1 200821 D00404 0490 BCECNHANXX TGCAGCTA TATCCTCT L004 R1 001.fastq.gz	0:51	A:350814963;C:322137968;G:296076522;T:388274118;N:135022	51	350814963	322137968	296076522	388274118	135022	SRX21337042	SRS18582316	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.67672	0.12184	0.77684	0.67617	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75283	75283	SRR25609947	SRX21337041	SRS18582316	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f23	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:23\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f23 Dm	f23 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F23-1_200821_D00404_0490_BCECNHANXX_CGATCAGT-CGTCTAAT_L004_R1_001.fastq.gz 2524F23-2_200821_D00404_0490_BCECNHANXX_CGATCAGT-CGTCTAAT_L005_R1_001.fastq.gz 2524F23-3_200821_D00404_0490_BCECNHANXX_CGATCAGT-CGTCTAAT_L006_R1_001.fastq.gz	fastq fastq fastq	1310635689.0	25698739.0	2524F23 1 200821 D00404 0490 BCECNHANXX CGATCAGT CGTCTAAT L004 R1 001.fastq.gz	0:51	A:329845205;C:319621549;G:290294319;T:370745436;N:129180	51	329845205	319621549	290294319	370745436	129180	SRX21337041	SRS18582316	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.65504	0.15018	0.76441	0.55473	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75284	75284	SRR25609948	SRX21337040	SRS18582315	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f22	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:22\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f22 Dl	f22 Dl	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F21-1_200821_D00404_0490_BCECNHANXX_CGATCAGT-AAGGAGTA_L004_R1_001.fastq.gz 2524F21-2_200821_D00404_0490_BCECNHANXX_CGATCAGT-AAGGAGTA_L005_R1_001.fastq.gz 2524F21-3_200821_D00404_0490_BCECNHANXX_CGATCAGT-AAGGAGTA_L006_R1_001.fastq.gz	fastq fastq fastq	1367103399.0	26805949.0	2524F21 1 200821 D00404 0490 BCECNHANXX CGATCAGT AAGGAGTA L004 R1 001.fastq.gz	0:51	A:348496475;C:329219887;G:304682170;T:384569914;N:134953	51	348496475	329219887	304682170	384569914	134953	SRX21337040	SRS18582315	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.69234	0.1751	0.75976	0.59565	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75285	75285	SRR25609949	SRX21337039	SRS18582315	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f22	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:22\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f22 Dp	f22 Dp	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F20-1_200821_D00404_0490_BCECNHANXX_CGATCAGT-ACTGCATA_L004_R1_001.fastq.gz 2524F20-2_200821_D00404_0490_BCECNHANXX_CGATCAGT-ACTGCATA_L005_R1_001.fastq.gz 2524F20-3_200821_D00404_0490_BCECNHANXX_CGATCAGT-ACTGCATA_L006_R1_001.fastq.gz	fastq fastq fastq	1391179938.0	27278038.0	2524F20 1 200821 D00404 0490 BCECNHANXX CGATCAGT ACTGCATA L004 R1 001.fastq.gz	0:51	A:358063871;C:331395885;G:307106587;T:394476102;N:137493	51	358063871	331395885	307106587	394476102	137493	SRX21337039	SRS18582315	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.70059	0.17705	0.77565	0.58748	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75286	75286	SRR25609950	SRX21337038	SRS18582314	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f20	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:20\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f20 Dc	f20 Dc	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F5-1_200821_D00404_0490_BCECNHANXX_ACTGAGCG-AAGGAGTA_L004_R1_001.fastq.gz 2524F5-2_200821_D00404_0490_BCECNHANXX_ACTGAGCG-AAGGAGTA_L005_R1_001.fastq.gz 2524F5-3_200821_D00404_0490_BCECNHANXX_ACTGAGCG-AAGGAGTA_L006_R1_001.fastq.gz	fastq fastq fastq	1286333577.0	25222227.0	2524F5 1 200821 D00404 0490 BCECNHANXX ACTGAGCG AAGGAGTA L004 R1 001.fastq.gz	0:51	A:325258798;C:312379944;G:283846256;T:364724064;N:124515	51	325258798	312379944	283846256	364724064	124515	SRX21337038	SRS18582314	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.65236	0.1239	0.78612	0.66212	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	Nervous System
75287	75287	SRR25609951	SRX21337037	SRS18582314	SRP454447	PRJNA964500	Danio rerio telencephalon sequencing	PRJNA964500	Whole Genome Sequencing	We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.				f20	strain:Tgvglut1:GFP; vglut2:DsRed\|dev stage:adult\|collection date:2020 07 28/2020 09 08\|geo loc name:Switzerland\|sex:NA\|tissue:telencephalon\|collected by:Chie Satou\|genotype:Tgvglut1:GFP;vglut2:DsRed\|fish:20\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio: adult telencephalon	f20 Dm	f20 Dm	RNA extraction of microdissected tissue; QC with RNA Pico Chip; library prepared with SmartSe2 protocol home made Tn5			RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP454447		2524F2-1_200821_D00404_0490_BCECNHANXX_ACTGAGCG-TATCCTCT_L004_R1_001.fastq.gz 2524F2-2_200821_D00404_0490_BCECNHANXX_ACTGAGCG-TATCCTCT_L005_R1_001.fastq.gz 2524F2-3_200821_D00404_0490_BCECNHANXX_ACTGAGCG-TATCCTCT_L006_R1_001.fastq.gz	fastq fastq fastq	1299221379.0	25474929.0	2524F2 1 200821 D00404 0490 BCECNHANXX ACTGAGCG TATCCTCT L004 R1 001.fastq.gz	0:51	A:331380237;C:312514649;G:287027828;T:368171190;N:127475	51	331380237	312514649	287027828	368171190	127475	SRX21337037	SRS18582314	SRA1690795	Friedrich Miescher Institute for Biomedical Research\|Neurobiology	Friedrich Miescher Institute for Biomedical Research	1	0.67545	0.15898	0.75672	0.59546	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Switzerland	2023-08-11	Adult	Adult	Brain	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");;