metadata: run_metadata: 650 rows where experiment.library_layout = "SINGLE", technology = "smartseq" and tissue

650 rows where experiment.library_layout = "SINGLE", technology = "smartseq" and tissue_curation = "Brain"

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.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
10237	10237	ERR7131169	ERX6698608	ERS8070397	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F8 Nega	SAMEA10418613	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418613\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F8 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 8\|organism part:olfactory bulb\|sample name:E MTAB 11083:F8 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F8 Nega s	F8 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F22-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-CTAAGCCT_L006_R1_001.fastq.gz	fastq	658093749.0	12903799.0	E MTAB 11083:2874F22 1 210715 D00404 0538 BCD91CANXX TCGACGTC CTAAGCCT L006	0:51 1:0	A:173355262;C:152464129;G:147489024;T:184739885;N:45449	51	0	173355262	152464129	147489024	184739885	45449	ERX6698608	ERS8070397	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.78328	0.15147	0.71289	0.53671	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10238	10238	ERR7131170	ERX6698608	ERS8070397	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F8 Nega	SAMEA10418613	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418613\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F8 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 8\|organism part:olfactory bulb\|sample name:E MTAB 11083:F8 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F8 Nega s	F8 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F22-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-CTAAGCCT_L007_R1_001.fastq.gz	fastq	661103769.0	12962819.0	E MTAB 11083:2874F22 2 210715 D00404 0538 BCD91CANXX TCGACGTC CTAAGCCT L007	0:51 1:0	A:174223249;C:153223284;G:148276805;T:185335092;N:45339	51	0	174223249	153223284	148276805	185335092	45339	ERX6698608	ERS8070397	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.78539	0.15054	0.70897	0.5322	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10239	10239	ERR7131167	ERX6698607	ERS8070396	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F8 mCherry GFP	SAMEA10418612	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418612\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F8 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 8\|organism part:olfactory bulb\|sample name:E MTAB 11083:F8 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F8 mCherry GFP s	F8 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F24-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-TCTCTCCG_L006_R1_001.fastq.gz	fastq	693183636.0	13591836.0	E MTAB 11083:2874F24 1 210715 D00404 0538 BCD91CANXX TCGACGTC TCTCTCCG L006	0:51 1:0	A:183977687;C:159275153;G:153149826;T:196732022;N:48948	51	0	183977687	159275153	153149826	196732022	48948	ERX6698607	ERS8070396	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.68942	0.15593	0.75828	0.51858	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10240	10240	ERR7131168	ERX6698607	ERS8070396	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F8 mCherry GFP	SAMEA10418612	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418612\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F8 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 8\|organism part:olfactory bulb\|sample name:E MTAB 11083:F8 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F8 mCherry GFP s	F8 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F24-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-TCTCTCCG_L007_R1_001.fastq.gz	fastq	696648678.0	13659778.0	E MTAB 11083:2874F24 2 210715 D00404 0538 BCD91CANXX TCGACGTC TCTCTCCG L007	0:51 1:0	A:184971832;C:160126524;G:154012023;T:197490098;N:48201	51	0	184971832	160126524	154012023	197490098	48201	ERX6698607	ERS8070396	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.6906	0.15634	0.75909	0.51346	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10241	10241	ERR7131165	ERX6698606	ERS8070395	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F8 mCherry	SAMEA10418611	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418611\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F8 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 8\|organism part:olfactory bulb\|sample name:E MTAB 11083:F8 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F8 mCherry s	F8 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F23-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-CGTCTAAT_L006_R1_001.fastq.gz	fastq	667760646.0	13093346.0	E MTAB 11083:2874F23 1 210715 D00404 0538 BCD91CANXX TCGACGTC CGTCTAAT L006	0:51 1:0	A:179948739;C:150541918;G:145038845;T:192184092;N:47052	51	0	179948739	150541918	145038845	192184092	47052	ERX6698606	ERS8070395	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.71661	0.19774	0.74576	0.52117	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10242	10242	ERR7131166	ERX6698606	ERS8070395	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F8 mCherry	SAMEA10418611	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418611\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F8 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 8\|organism part:olfactory bulb\|sample name:E MTAB 11083:F8 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F8 mCherry s	F8 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F23-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-CGTCTAAT_L007_R1_001.fastq.gz	fastq	670970484.0	13156284.0	E MTAB 11083:2874F23 2 210715 D00404 0538 BCD91CANXX TCGACGTC CGTCTAAT L007	0:51 1:0	A:180906557;C:151329492;G:145816347;T:192872804;N:45284	51	0	180906557	151329492	145816347	192872804	45284	ERX6698606	ERS8070395	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.71682	0.19902	0.74517	0.52618	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10243	10243	ERR7131163	ERX6698605	ERS8070394	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F7 Nega	SAMEA10418610	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418610\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F7 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 7\|organism part:olfactory bulb\|sample name:E MTAB 11083:F7 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F7 Nega s	F7 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F19-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-GTAAGGAG_L006_R1_001.fastq.gz	fastq	652205238.0	12788338.0	E MTAB 11083:2874F19 1 210715 D00404 0538 BCD91CANXX TCGACGTC GTAAGGAG L006	0:51 1:0	A:173730405;C:149044598;G:145436777;T:183946928;N:46530	51	0	173730405	149044598	145436777	183946928	46530	ERX6698605	ERS8070394	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.80595	0.17309	0.71003	0.53696	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10244	10244	ERR7131164	ERX6698605	ERS8070394	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F7 Nega	SAMEA10418610	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418610\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F7 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 7\|organism part:olfactory bulb\|sample name:E MTAB 11083:F7 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F7 Nega s	F7 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F19-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-GTAAGGAG_L007_R1_001.fastq.gz	fastq	655593423.0	12854773.0	E MTAB 11083:2874F19 2 210715 D00404 0538 BCD91CANXX TCGACGTC GTAAGGAG L007	0:51 1:0	A:174715119;C:149844974;G:146250446;T:184737535;N:45349	51	0	174715119	149844974	146250446	184737535	45349	ERX6698605	ERS8070394	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.80585	0.17497	0.71078	0.53767	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10245	10245	ERR7131161	ERX6698604	ERS8070393	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F7 mCherry GFP	SAMEA10418609	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418609\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F7 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 7\|organism part:olfactory bulb\|sample name:E MTAB 11083:F7 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F7 mCherry GFP s	F7 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F21-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-AAGGAGTA_L006_R1_001.fastq.gz	fastq	661067151.0	12962101.0	E MTAB 11083:2874F21 1 210715 D00404 0538 BCD91CANXX TCGACGTC AAGGAGTA L006	0:51 1:0	A:168281419;C:157701209;G:153487197;T:181550252;N:47074	51	0	168281419	157701209	153487197	181550252	47074	ERX6698604	ERS8070393	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.39074	0.11592	0.82615	0.5252	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10246	10246	ERR7131162	ERX6698604	ERS8070393	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F7 mCherry GFP	SAMEA10418609	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418609\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F7 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 7\|organism part:olfactory bulb\|sample name:E MTAB 11083:F7 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F7 mCherry GFP s	F7 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F21-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-AAGGAGTA_L007_R1_001.fastq.gz	fastq	665709018.0	13053118.0	E MTAB 11083:2874F21 2 210715 D00404 0538 BCD91CANXX TCGACGTC AAGGAGTA L007	0:51 1:0	A:169539998;C:158884603;G:154624803;T:182614264;N:45350	51	0	169539998	158884603	154624803	182614264	45350	ERX6698604	ERS8070393	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.38966	0.1152	0.8258	0.53305	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10247	10247	ERR7131159	ERX6698603	ERS8070392	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F7 mCherry	SAMEA10418608	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418608\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F7 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 7\|organism part:olfactory bulb\|sample name:E MTAB 11083:F7 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F7 mCherry s	F7 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F20-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-ACTGCATA_L006_R1_001.fastq.gz	fastq	657813402.0	12898302.0	E MTAB 11083:2874F20 1 210715 D00404 0538 BCD91CANXX TCGACGTC ACTGCATA L006	0:51 1:0	A:175873489;C:149476129;G:143987770;T:188429588;N:46426	51	0	175873489	149476129	143987770	188429588	46426	ERX6698603	ERS8070392	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.70507	0.2048	0.75923	0.52828	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10248	10248	ERR7131160	ERX6698603	ERS8070392	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F7 mCherry	SAMEA10418608	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418608\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F7 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 7\|organism part:olfactory bulb\|sample name:E MTAB 11083:F7 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F7 mCherry s	F7 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F20-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-ACTGCATA_L007_R1_001.fastq.gz	fastq	660303426.0	12947126.0	E MTAB 11083:2874F20 2 210715 D00404 0538 BCD91CANXX TCGACGTC ACTGCATA L007	0:51 1:0	A:176607119;C:150065781;G:144613110;T:188972809;N:44607	51	0	176607119	150065781	144613110	188972809	44607	ERX6698603	ERS8070392	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.70705	0.20314	0.75852	0.52949	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10249	10249	ERR7131157	ERX6698602	ERS8070391	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F6 Nega	SAMEA10418607	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418607\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F6 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 6\|organism part:olfactory bulb\|sample name:E MTAB 11083:F6 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F6 Nega s	F6 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F16-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-TCTCTCCG_L006_R1_001.fastq.gz	fastq	669627450.0	13129950.0	E MTAB 11083:2874F16 1 210715 D00404 0538 BCD91CANXX TGCAGCTA TCTCTCCG L006	0:51 1:0	A:177483937;C:154097051;G:148063012;T:189935690;N:47760	51	0	177483937	154097051	148063012	189935690	47760	ERX6698602	ERS8070391	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.77183	0.16001	0.71467	0.53352	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10250	10250	ERR7131158	ERX6698602	ERS8070391	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F6 Nega	SAMEA10418607	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418607\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F6 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 6\|organism part:olfactory bulb\|sample name:E MTAB 11083:F6 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F6 Nega s	F6 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F16-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-TCTCTCCG_L007_R1_001.fastq.gz	fastq	671615073.0	13168923.0	E MTAB 11083:2874F16 2 210715 D00404 0538 BCD91CANXX TGCAGCTA TCTCTCCG L007	0:51 1:0	A:178109157;C:154619024;G:148595207;T:190246469;N:45216	51	0	178109157	154619024	148595207	190246469	45216	ERX6698602	ERS8070391	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.77284	0.15963	0.71569	0.53038	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10251	10251	ERR7131155	ERX6698601	ERS8070390	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F6 mCherry GFP	SAMEA10418606	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418606\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F6 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 6\|organism part:olfactory bulb\|sample name:E MTAB 11083:F6 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F6 mCherry GFP s	F6 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F18-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-TATCCTCT_L006_R1_001.fastq.gz	fastq	667663542.0	13091442.0	E MTAB 11083:2874F18 1 210715 D00404 0538 BCD91CANXX TCGACGTC TATCCTCT L006	0:51 1:0	A:177646483;C:152747528;G:146388226;T:190833951;N:47354	51	0	177646483	152747528	146388226	190833951	47354	ERX6698601	ERS8070390	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.67964	0.18123	0.77193	0.53313	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10252	10252	ERR7131156	ERX6698601	ERS8070390	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F6 mCherry GFP	SAMEA10418606	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418606\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F6 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 6\|organism part:olfactory bulb\|sample name:E MTAB 11083:F6 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F6 mCherry GFP s	F6 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F18-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-TATCCTCT_L007_R1_001.fastq.gz	fastq	670170141.0	13140591.0	E MTAB 11083:2874F18 2 210715 D00404 0538 BCD91CANXX TCGACGTC TATCCTCT L007	0:51 1:0	A:178425395;C:153363855;G:147033779;T:191300976;N:46136	51	0	178425395	153363855	147033779	191300976	46136	ERX6698601	ERS8070390	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.67922	0.18101	0.77141	0.53601	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10253	10253	ERR7131153	ERX6698600	ERS8070389	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F6 mCherry	SAMEA10418605	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418605\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F6 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 6\|organism part:olfactory bulb\|sample name:E MTAB 11083:F6 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F6 mCherry s	F6 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F17-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-CTCTCTAT_L006_R1_001.fastq.gz	fastq	677617008.0	13286608.0	E MTAB 11083:2874F17 1 210715 D00404 0538 BCD91CANXX TCGACGTC CTCTCTAT L006	0:51 1:0	A:181785899;C:152797687;G:147070676;T:195914808;N:47938	51	0	181785899	152797687	147070676	195914808	47938	ERX6698600	ERS8070389	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.68298	0.1953	0.76292	0.5395	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10254	10254	ERR7131154	ERX6698600	ERS8070389	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F6 mCherry	SAMEA10418605	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418605\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F6 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 6\|organism part:olfactory bulb\|sample name:E MTAB 11083:F6 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F6 mCherry s	F6 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F17-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-CTCTCTAT_L007_R1_001.fastq.gz	fastq	679922973.0	13331823.0	E MTAB 11083:2874F17 2 210715 D00404 0538 BCD91CANXX TCGACGTC CTCTCTAT L007	0:51 1:0	A:182567819;C:153380607;G:147589890;T:196337722;N:46935	51	0	182567819	153380607	147589890	196337722	46935	ERX6698600	ERS8070389	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.68391	0.19726	0.76299	0.54099	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10255	10255	ERR7131151	ERX6698599	ERS8070388	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F5 Nega	SAMEA10418604	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418604\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F5 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 5\|organism part:olfactory bulb\|sample name:E MTAB 11083:F5 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F5 Nega s	F5 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F13-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-AAGGAGTA_L006_R1_001.fastq.gz	fastq	620316315.0	12163065.0	E MTAB 11083:2874F13 1 210715 D00404 0538 BCD91CANXX TGCAGCTA AAGGAGTA L006	0:51 1:0	A:165967355;C:141072216;G:136931219;T:176301963;N:43562	51	0	165967355	141072216	136931219	176301963	43562	ERX6698599	ERS8070388	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.78924	0.17457	0.71934	0.53563	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10256	10256	ERR7131152	ERX6698599	ERS8070388	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F5 Nega	SAMEA10418604	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418604\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F5 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 5\|organism part:olfactory bulb\|sample name:E MTAB 11083:F5 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F5 Nega s	F5 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F13-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-AAGGAGTA_L007_R1_001.fastq.gz	fastq	623905338.0	12233438.0	E MTAB 11083:2874F13 2 210715 D00404 0538 BCD91CANXX TGCAGCTA AAGGAGTA L007	0:51 1:0	A:166996253;C:141937637;G:137825206;T:177103504;N:42738	51	0	166996253	141937637	137825206	177103504	42738	ERX6698599	ERS8070388	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.78975	0.17387	0.72153	0.54149	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10257	10257	ERR7131149	ERX6698598	ERS8070387	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F5 mCherry GFP	SAMEA10418603	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418603\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F5 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 5\|organism part:olfactory bulb\|sample name:E MTAB 11083:F5 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F5 mCherry GFP s	F5 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F15-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CGTCTAAT_L006_R1_001.fastq.gz	fastq	670154841.0	13140291.0	E MTAB 11083:2874F15 1 210715 D00404 0538 BCD91CANXX TGCAGCTA CGTCTAAT L006	0:51 1:0	A:182457480;C:149175456;G:144548173;T:193927470;N:46262	51	0	182457480	149175456	144548173	193927470	46262	ERX6698598	ERS8070387	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.71875	0.18671	0.76047	0.52398	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10258	10258	ERR7131150	ERX6698598	ERS8070387	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F5 mCherry GFP	SAMEA10418603	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418603\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F5 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 5\|organism part:olfactory bulb\|sample name:E MTAB 11083:F5 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F5 mCherry GFP s	F5 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F15-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CGTCTAAT_L007_R1_001.fastq.gz	fastq	674202048.0	13219648.0	E MTAB 11083:2874F15 2 210715 D00404 0538 BCD91CANXX TGCAGCTA CGTCTAAT L007	0:51 1:0	A:183639511;C:150168226;G:145502071;T:194847755;N:44485	51	0	183639511	150168226	145502071	194847755	44485	ERX6698598	ERS8070387	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.72111	0.18813	0.76378	0.5258	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10259	10259	ERR7131147	ERX6698597	ERS8070386	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F5 mCherry	SAMEA10418602	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418602\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F5 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 5\|organism part:olfactory bulb\|sample name:E MTAB 11083:F5 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F5 mCherry s	F5 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F14-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CTAAGCCT_L006_R1_001.fastq.gz	fastq	615458259.0	12067809.0	E MTAB 11083:2874F14 1 210715 D00404 0538 BCD91CANXX TGCAGCTA CTAAGCCT L006	0:51 1:0	A:165108582;C:139178883;G:134070672;T:177059757;N:40365	51	0	165108582	139178883	134070672	177059757	40365	ERX6698597	ERS8070386	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.69017	0.1977	0.77193	0.53352	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10260	10260	ERR7131148	ERX6698597	ERS8070386	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F5 mCherry	SAMEA10418602	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418602\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F5 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 5\|organism part:olfactory bulb\|sample name:E MTAB 11083:F5 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F5 mCherry s	F5 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F14-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CTAAGCCT_L007_R1_001.fastq.gz	fastq	619061613.0	12138463.0	E MTAB 11083:2874F14 2 210715 D00404 0538 BCD91CANXX TGCAGCTA CTAAGCCT L007	0:51 1:0	A:166167516;C:140058774;G:134972850;T:177822733;N:39740	51	0	166167516	140058774	134972850	177822733	39740	ERX6698597	ERS8070386	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.69118	0.20019	0.7707	0.52174	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10261	10261	ERR7131145	ERX6698596	ERS8070385	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F4 Nega	SAMEA10418601	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418601\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F4 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 4\|organism part:olfactory bulb\|sample name:E MTAB 11083:F4 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F4 Nega s	F4 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F10-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-TATCCTCT_L006_R1_001.fastq.gz	fastq	652536687.0	12794837.0	E MTAB 11083:2874F10 1 210715 D00404 0538 BCD91CANXX TGCAGCTA TATCCTCT L006	0:51 1:0	A:178033231;C:144661707;G:139876661;T:189921085;N:44003	51	0	178033231	144661707	139876661	189921085	44003	ERX6698596	ERS8070385	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.76201	0.2508	0.71299	0.53379	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10262	10262	ERR7131146	ERX6698596	ERS8070385	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F4 Nega	SAMEA10418601	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418601\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F4 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 4\|organism part:olfactory bulb\|sample name:E MTAB 11083:F4 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F4 Nega s	F4 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F10-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-TATCCTCT_L007_R1_001.fastq.gz	fastq	655278957.0	12848607.0	E MTAB 11083:2874F10 2 210715 D00404 0538 BCD91CANXX TGCAGCTA TATCCTCT L007	0:51 1:0	A:178938002;C:145332613;G:140527756;T:190437189;N:43397	51	0	178938002	145332613	140527756	190437189	43397	ERX6698596	ERS8070385	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.76188	0.25356	0.71344	0.53081	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10263	10263	ERR7131143	ERX6698595	ERS8070384	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F4 mCherry GFP	SAMEA10418600	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418600\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F4 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 4\|organism part:olfactory bulb\|sample name:E MTAB 11083:F4 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F4 mCherry GFP s	F4 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F12-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-ACTGCATA_L006_R1_001.fastq.gz	fastq	297921855.0	5841605.0	E MTAB 11083:2874F12 1 210715 D00404 0538 BCD91CANXX TGCAGCTA ACTGCATA L006	0:51 1:0	A:82400724;C:65517496;G:64603058;T:85384480;N:16097	51	0	82400724	65517496	64603058	85384480	16097	ERX6698595	ERS8070384	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.72496	0.20794	0.81223	0.52529	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10264	10264	ERR7131144	ERX6698595	ERS8070384	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F4 mCherry GFP	SAMEA10418600	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418600\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F4 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 4\|organism part:olfactory bulb\|sample name:E MTAB 11083:F4 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F4 mCherry GFP s	F4 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F12-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-ACTGCATA_L007_R1_001.fastq.gz	fastq	309412971.0	6066921.0	E MTAB 11083:2874F12 2 210715 D00404 0538 BCD91CANXX TGCAGCTA ACTGCATA L007	0:51 1:0	A:85531271;C:68164437;G:67129209;T:88573210;N:14844	51	0	85531271	68164437	67129209	88573210	14844	ERX6698595	ERS8070384	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.7245	0.20724	0.80468	0.52791	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10265	10265	ERR7131141	ERX6698594	ERS8070383	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F4 mCherry	SAMEA10418599	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418599\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F4 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 4\|organism part:olfactory bulb\|sample name:E MTAB 11083:F4 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F4 mCherry s	F4 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F11-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-GTAAGGAG_L006_R1_001.fastq.gz	fastq	672319791.0	13182741.0	E MTAB 11083:2874F11 1 210715 D00404 0538 BCD91CANXX TGCAGCTA GTAAGGAG L006	0:51 1:0	A:181508034;C:150928549;G:146124085;T:193711358;N:47765	51	0	181508034	150928549	146124085	193711358	47765	ERX6698594	ERS8070383	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.71726	0.19842	0.74986	0.53363	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10266	10266	ERR7131142	ERX6698594	ERS8070383	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F4 mCherry	SAMEA10418599	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418599\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F4 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 4\|organism part:olfactory bulb\|sample name:E MTAB 11083:F4 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F4 mCherry s	F4 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F11-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-GTAAGGAG_L007_R1_001.fastq.gz	fastq	675486075.0	13244825.0	E MTAB 11083:2874F11 2 210715 D00404 0538 BCD91CANXX TGCAGCTA GTAAGGAG L007	0:51 1:0	A:182462261;C:151688554;G:146902713;T:194385945;N:46602	51	0	182462261	151688554	146902713	194385945	46602	ERX6698594	ERS8070383	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.71745	0.19727	0.74805	0.53092	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10267	10267	ERR7131139	ERX6698593	ERS8070382	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F3 Nega	SAMEA10418598	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418598\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F3 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 3\|organism part:olfactory bulb\|sample name:E MTAB 11083:F3 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F3 Nega s	F3 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F7-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-CGTCTAAT_L006_R1_001.fastq.gz	fastq	630093627.0	12354777.0	E MTAB 11083:2874F7 1 210715 D00404 0538 BCD91CANXX CGATCAGT CGTCTAAT L006	0:51 1:0	A:165132739;C:146179836;G:142796880;T:175940613;N:43559	51	0	165132739	146179836	142796880	175940613	43559	ERX6698593	ERS8070382	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.81672	0.15219	0.71277	0.52461	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10268	10268	ERR7131140	ERX6698593	ERS8070382	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F3 Nega	SAMEA10418598	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418598\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F3 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 3\|organism part:olfactory bulb\|sample name:E MTAB 11083:F3 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F3 Nega s	F3 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F7-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-CGTCTAAT_L007_R1_001.fastq.gz	fastq	632305242.0	12398142.0	E MTAB 11083:2874F7 2 210715 D00404 0538 BCD91CANXX CGATCAGT CGTCTAAT L007	0:51 1:0	A:165832174;C:146751895;G:143384539;T:176293313;N:43321	51	0	165832174	146751895	143384539	176293313	43321	ERX6698593	ERS8070382	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.81791	0.15444	0.7151	0.52585	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10269	10269	ERR7131137	ERX6698592	ERS8070381	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F3 mCherry GFP	SAMEA10418597	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418597\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F3 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 3\|organism part:olfactory bulb\|sample name:E MTAB 11083:F3 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F3 mCherry GFP s	F3 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F9-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CTCTCTAT_L006_R1_001.fastq.gz	fastq	660379620.0	12948620.0	E MTAB 11083:2874F9 1 210715 D00404 0538 BCD91CANXX TGCAGCTA CTCTCTAT L006	0:51 1:0	A:178482695;C:147417787;G:143797476;T:190635173;N:46489	51	0	178482695	147417787	143797476	190635173	46489	ERX6698592	ERS8070381	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.65635	0.17778	0.76899	0.52957	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10270	10270	ERR7131138	ERX6698592	ERS8070381	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F3 mCherry GFP	SAMEA10418597	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418597\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F3 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 3\|organism part:olfactory bulb\|sample name:E MTAB 11083:F3 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F3 mCherry GFP s	F3 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F9-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CTCTCTAT_L007_R1_001.fastq.gz	fastq	662411307.0	12988457.0	E MTAB 11083:2874F9 2 210715 D00404 0538 BCD91CANXX TGCAGCTA CTCTCTAT L007	0:51 1:0	A:179158323;C:147942300;G:144319925;T:190945370;N:45389	51	0	179158323	147942300	144319925	190945370	45389	ERX6698592	ERS8070381	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.65813	0.17896	0.77076	0.52835	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10271	10271	ERR7131135	ERX6698591	ERS8070380	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F3 mCherry	SAMEA10418596	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418596\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F3 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 3\|organism part:olfactory bulb\|sample name:E MTAB 11083:F3 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F3 mCherry s	F3 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F8-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-TCTCTCCG_L006_R1_001.fastq.gz	fastq	698608353.0	13698203.0	E MTAB 11083:2874F8 1 210715 D00404 0538 BCD91CANXX CGATCAGT TCTCTCCG L006	0:51 1:0	A:188718612;C:156814081;G:151125083;T:201901570;N:49007	51	0	188718612	156814081	151125083	201901570	49007	ERX6698591	ERS8070380	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.70185	0.21547	0.75588	0.53853	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10272	10272	ERR7131136	ERX6698591	ERS8070380	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F3 mCherry	SAMEA10418596	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418596\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F3 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 3\|organism part:olfactory bulb\|sample name:E MTAB 11083:F3 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F3 mCherry s	F3 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F8-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-TCTCTCCG_L007_R1_001.fastq.gz	fastq	699869175.0	13722925.0	E MTAB 11083:2874F8 2 210715 D00404 0538 BCD91CANXX CGATCAGT TCTCTCCG L007	0:51 1:0	A:189192315;C:157176897;G:151498983;T:201952867;N:48113	51	0	189192315	157176897	151498983	201952867	48113	ERX6698591	ERS8070380	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.70221	0.21684	0.75621	0.53787	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10273	10273	ERR7131133	ERX6698590	ERS8070379	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F2 Nega	SAMEA10418595	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418595\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F2 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 2\|organism part:olfactory bulb\|sample name:E MTAB 11083:F2 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F2 Nega s	F2 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F4-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-ACTGCATA_L006_R1_001.fastq.gz	fastq	573812985.0	11251235.0	E MTAB 11083:2874F4 1 210715 D00404 0538 BCD91CANXX CGATCAGT ACTGCATA L006	0:51 1:0	A:150716404;C:132203167;G:129732968;T:161120057;N:40389	51	0	150716404	132203167	129732968	161120057	40389	ERX6698590	ERS8070379	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.81899	0.17302	0.72281	0.54315	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10274	10274	ERR7131134	ERX6698590	ERS8070379	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F2 Nega	SAMEA10418595	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418595\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F2 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 2\|organism part:olfactory bulb\|sample name:E MTAB 11083:F2 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F2 Nega s	F2 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F4-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-ACTGCATA_L007_R1_001.fastq.gz	fastq	576184587.0	11297737.0	E MTAB 11083:2874F4 2 210715 D00404 0538 BCD91CANXX CGATCAGT ACTGCATA L007	0:51 1:0	A:151387408;C:132788210;G:130392043;T:161577529;N:39397	51	0	151387408	132788210	130392043	161577529	39397	ERX6698590	ERS8070379	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.81999	0.17082	0.72196	0.54505	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10275	10275	ERR7131131	ERX6698589	ERS8070378	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F2 mCherry GFP	SAMEA10418594	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418594\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F2 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 2\|organism part:olfactory bulb\|sample name:E MTAB 11083:F2 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F2 mCherry GFP s	F2 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F6-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-CTAAGCCT_L006_R1_001.fastq.gz	fastq	654811032.0	12839432.0	E MTAB 11083:2874F6 1 210715 D00404 0538 BCD91CANXX CGATCAGT CTAAGCCT L006	0:51 1:0	A:177403486;C:146202733;G:142207545;T:188951373;N:45895	51	0	177403486	146202733	142207545	188951373	45895	ERX6698589	ERS8070378	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.67854	0.21407	0.76104	0.52713	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10276	10276	ERR7131132	ERX6698589	ERS8070378	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F2 mCherry GFP	SAMEA10418594	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418594\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F2 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 2\|organism part:olfactory bulb\|sample name:E MTAB 11083:F2 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F2 mCherry GFP s	F2 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F6-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-CTAAGCCT_L007_R1_001.fastq.gz	fastq	656911926.0	12880626.0	E MTAB 11083:2874F6 2 210715 D00404 0538 BCD91CANXX CGATCAGT CTAAGCCT L007	0:51 1:0	A:178119212;C:146730132;G:142725348;T:189293212;N:44022	51	0	178119212	146730132	142725348	189293212	44022	ERX6698589	ERS8070378	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.68162	0.21431	0.761	0.5071	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10277	10277	ERR7131129	ERX6698588	ERS8070377	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F2 mCherry	SAMEA10418593	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418593\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F2 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 2\|organism part:olfactory bulb\|sample name:E MTAB 11083:F2 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F2 mCherry s	F2 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F5-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-AAGGAGTA_L006_R1_001.fastq.gz	fastq	607851558.0	11918658.0	E MTAB 11083:2874F5 1 210715 D00404 0538 BCD91CANXX CGATCAGT AAGGAGTA L006	0:51 1:0	A:164814138;C:136071648;G:132945950;T:173976881;N:42941	51	0	164814138	136071648	132945950	173976881	42941	ERX6698588	ERS8070377	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.78967	0.18905	0.73241	0.52347	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10278	10278	ERR7131130	ERX6698588	ERS8070377	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F2 mCherry	SAMEA10418593	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418593\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F2 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 2\|organism part:olfactory bulb\|sample name:E MTAB 11083:F2 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F2 mCherry s	F2 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F5-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-AAGGAGTA_L007_R1_001.fastq.gz	fastq	610931805.0	11979055.0	E MTAB 11083:2874F5 2 210715 D00404 0538 BCD91CANXX CGATCAGT AAGGAGTA L007	0:51 1:0	A:165714775;C:136822925;G:133684294;T:174667814;N:41997	51	0	165714775	136822925	133684294	174667814	41997	ERX6698588	ERS8070377	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.78869	0.18885	0.73156	0.51691	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10279	10279	ERR7131127	ERX6698587	ERS8070376	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F1 Nega	SAMEA10418592	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418592\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F1 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 1\|organism part:olfactory bulb\|sample name:E MTAB 11083:F1 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F1 Nega s	F1 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F1-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-CTCTCTAT_L006_R1_001.fastq.gz	fastq	619561872.0	12148272.0	E MTAB 11083:2874F1 1 210715 D00404 0538 BCD91CANXX CGATCAGT CTCTCTAT L006	0:51 1:0	A:164385545;C:141746313;G:138163219;T:175223323;N:43472	51	0	164385545	141746313	138163219	175223323	43472	ERX6698587	ERS8070376	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.80258	0.17703	0.72614	0.53483	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10280	10280	ERR7131128	ERX6698587	ERS8070376	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F1 Nega	SAMEA10418592	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418592\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F1 Nega\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry /GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 1\|organism part:olfactory bulb\|sample name:E MTAB 11083:F1 Nega\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F1 Nega s	F1 Nega s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry /GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F1-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-CTCTCTAT_L007_R1_001.fastq.gz	fastq	621481971.0	12185921.0	E MTAB 11083:2874F1 2 210715 D00404 0538 BCD91CANXX CGATCAGT CTCTCTAT L007	0:51 1:0	A:165030774;C:142231469;G:138651078;T:175527080;N:41570	51	0	165030774	142231469	138651078	175527080	41570	ERX6698587	ERS8070376	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.80248	0.17699	0.726	0.53711	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10281	10281	ERR7131125	ERX6698586	ERS8070375	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F1 mCherry GFP	SAMEA10418591	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418591\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F1 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 1\|organism part:olfactory bulb\|sample name:E MTAB 11083:F1 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F1 mCherry GFP s	F1 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F3-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-GTAAGGAG_L006_R1_001.fastq.gz	fastq	651189369.0	12768419.0	E MTAB 11083:2874F3 1 210715 D00404 0538 BCD91CANXX CGATCAGT GTAAGGAG L006	0:51 1:0	A:176398415;C:145659111;G:142137610;T:186948280;N:45953	51	0	176398415	145659111	142137610	186948280	45953	ERX6698586	ERS8070375	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.69561	0.18489	0.75345	0.52316	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10282	10282	ERR7131126	ERX6698586	ERS8070375	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F1 mCherry GFP	SAMEA10418591	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418591\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F1 mCherry GFP\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP+\|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 1\|organism part:olfactory bulb\|sample name:E MTAB 11083:F1 mCherry GFP\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F1 mCherry GFP s	F1 mCherry GFP s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP+	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F3-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-GTAAGGAG_L007_R1_001.fastq.gz	fastq	653398944.0	12811744.0	E MTAB 11083:2874F3 2 210715 D00404 0538 BCD91CANXX CGATCAGT GTAAGGAG L007	0:51 1:0	A:177139734;C:146171766;G:142707146;T:187335475;N:44823	51	0	177139734	146171766	142707146	187335475	44823	ERX6698586	ERS8070375	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.69496	0.18414	0.75375	0.52317	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10283	10283	ERR7131123	ERX6698585	ERS8070374	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F1 mCherry	SAMEA10418590	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418590\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F1 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 1\|organism part:olfactory bulb\|sample name:E MTAB 11083:F1 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F1 mCherry s	F1 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F2-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-TATCCTCT_L006_R1_001.fastq.gz	fastq	613574319.0	12030869.0	E MTAB 11083:2874F2 1 210715 D00404 0538 BCD91CANXX CGATCAGT TATCCTCT L006	0:51 1:0	A:164891629;C:138401759;G:135818073;T:174419828;N:43030	51	0	164891629	138401759	135818073	174419828	43030	ERX6698585	ERS8070374	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.79499	0.21674	0.73359	0.52207	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
10284	10284	ERR7131124	ERX6698585	ERS8070374	ERP132560	PRJEB48218	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E-MTAB-11083	Transcriptome Analysis	To investigate the effects of rabies infection on neuronal gene expression we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07		Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	F1 mCherry	SAMEA10418590	Friedrich Miescher Institute for Biomedical Research	ENA first public:2021 12 01\|ENA last update:2021 12 01\|External Id:SAMEA10418590\|INSDC center alias:Friedrich Miescher Institute for Biomedical Research\|INSDC center name:Friedrich Miescher Institute for Biomedical Research\|INSDC first public:2021 12 01T00:23:59Z\|INSDC last update:2021 12 01T00:23:59Z\|INSDC status:public\|Submitter Id:E MTAB 11083:F1 mCherry\|age:9\|broker name:ArrayExpress\|cell type:GABAergic neuron\|common name:zebrafish\|developmental stage:adult\|fraction:mCherry+/GFP \|genotype:Tg[gad1b:Gal4 UAS:TVA mCherry]\|individual:pool 1\|organism part:olfactory bulb\|sample name:E MTAB 11083:F1 mCherry\|sex:mixed\|stimulus:injected with EnvA RV GFP\|strain:Ab x Tu x TL x WIK									Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	E MTAB 11083:F1 mCherry s	F1 mCherry s	Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4 UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al Nature protocol 2014 with the following modifications: For cDNA pre amplification up to 10ng of RNA was used as input typically 1 3ng and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific 50C for 10min 80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation using in house purified Tn5 Picelli et al Genome Research 2014 and Illumina Nextera primers.	Experimental Factor: fraction:mCherry+/GFP	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP132560	Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb	ENA FIRST PUBLIC:2022 07 07\|ENA LAST UPDATE:2022 07 07	2874F2-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-TATCCTCT_L007_R1_001.fastq.gz	fastq	615666798.0	12071898.0	E MTAB 11083:2874F2 2 210715 D00404 0538 BCD91CANXX CGATCAGT TATCCTCT L007	0:51 1:0	A:165536502;C:138952758;G:136375193;T:174760659;N:41686	51	0	165536502	138952758	136375193	174760659	41686	ERX6698585	ERS8070374	ERA6757553	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	Friedrich Miescher Institute for Biomedical Research\|European Nucleotide Archive	1	0.7941	0.21645	0.73494	0.50761	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Switzerland	2021-12-01	Adult	Adult	Brain	Nervous System
29933	29933	SRR27592958	SRX23261722	SRS20163687	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep15	GSM8020230		source name:single dissected adult brain male\|tissue:single dissected adult brain male\|genotype:arid1b homozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep15	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain male		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain male\|genotype:arid1b homozygous	GSM8020230	GSM8020230: arid1b adult rep15; Danio rerio; RNA Seq	GSM8020230 r1	GSM8020230	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set2-hom_A8_S20_R1_001.fastq.gz	fastq	4265635010.0	42234010.0	GSM8020230 r1	0:101	A:1152569190;C:1002056793;G:969860357;T:1141141715;N:6955	101		1152569190	1002056793	969860357	1141141715	6955	SRX23261722	SRS20163687	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29934	29934	SRR27592959	SRX23261721	SRS20163686	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep14	GSM8020229		source name:single dissected adult brain male\|tissue:single dissected adult brain male\|genotype:arid1b homozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep14	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain male		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain male\|genotype:arid1b homozygous	GSM8020229	GSM8020229: arid1b adult rep14; Danio rerio; RNA Seq	GSM8020229 r1	GSM8020229	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set2-hom_A6_S18_R1_001.fastq.gz	fastq	1422969608.0	14088808.0	GSM8020229 r1	0:101	A:389767872;C:327820009;G:327097969;T:378282090;N:1668	101		389767872	327820009	327097969	378282090	1668	SRX23261721	SRS20163686	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29935	29935	SRR27592960	SRX23261720	SRS20163685	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep13	GSM8020228		source name:single dissected adult brain male\|tissue:single dissected adult brain male\|genotype:arid1b homozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep13	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain male		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain male\|genotype:arid1b homozygous	GSM8020228	GSM8020228: arid1b adult rep13; Danio rerio; RNA Seq	GSM8020228 r1	GSM8020228	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set2-hom_A4_S16_R1_001.fastq.gz	fastq	4331217239.0	42883339.0	GSM8020228 r1	0:101	A:1169654932;C:1016829715;G:986390612;T:1158335000;N:6980	101		1169654932	1016829715	986390612	1158335000	6980	SRX23261720	SRS20163685	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29936	29936	SRR27592961	SRX23261719	SRS20163684	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep12	GSM8020227		source name:single dissected adult brain male\|tissue:single dissected adult brain male\|genotype:arid1b homozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep12	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain male		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain male\|genotype:arid1b homozygous	GSM8020227	GSM8020227: arid1b adult rep12; Danio rerio; RNA Seq	GSM8020227 r1	GSM8020227	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set2-hom_A2_S14_R1_001.fastq.gz	fastq	820969107.0	8128407.0	GSM8020227 r1	0:101	A:229523100;C:185511734;G:179068656;T:226864374;N:1243	101		229523100	185511734	179068656	226864374	1243	SRX23261719	SRS20163684	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29937	29937	SRR27592962	SRX23261718	SRS20163683	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep11	GSM8020226		source name:single dissected adult brain male\|tissue:single dissected adult brain male\|genotype:arid1b heterozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep11	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain male		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain male\|genotype:arid1b heterozygous	GSM8020226	GSM8020226: arid1b adult rep11; Danio rerio; RNA Seq	GSM8020226 r1	GSM8020226	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set2-het_A7_S19_R1_001.fastq.gz	fastq	3609957150.0	35742150.0	GSM8020226 r1	0:101	A:997333826;C:818355353;G:803362992;T:990899286;N:5693	101		997333826	818355353	803362992	990899286	5693	SRX23261718	SRS20163683	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29938	29938	SRR27592963	SRX23261717	SRS20163682	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep10	GSM8020225		source name:single dissected adult brain male\|tissue:single dissected adult brain male\|genotype:arid1b heterozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep10	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain male		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain male\|genotype:arid1b heterozygous	GSM8020225	GSM8020225: arid1b adult rep10; Danio rerio; RNA Seq	GSM8020225 r1	GSM8020225	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set2-het_A5_S17_R1_001.fastq.gz	fastq	3177521913.0	31460613.0	GSM8020225 r1	0:101	A:869322737;C:728803554;G:719191487;T:860199264;N:4871	101		869322737	728803554	719191487	860199264	4871	SRX23261717	SRS20163682	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29939	29939	SRR27592964	SRX23261716	SRS20163681	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep9	GSM8020224		source name:single dissected adult brain male\|tissue:single dissected adult brain male\|genotype:arid1b heterozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep9	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain male		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain male\|genotype:arid1b heterozygous	GSM8020224	GSM8020224: arid1b adult rep9; Danio rerio; RNA Seq	GSM8020224 r1	GSM8020224	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set2-het_A3_S15_R1_001.fastq.gz	fastq	3681640688.0	36451888.0	GSM8020224 r1	0:101	A:972550652;C:881056608;G:858084187;T:969943492;N:5749	101		972550652	881056608	858084187	969943492	5749	SRX23261716	SRS20163681	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29940	29940	SRR27592965	SRX23261715	SRS20163679	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep8	GSM8020223		source name:single dissected adult brain male\|tissue:single dissected adult brain male\|genotype:arid1b heterozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep8	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain male		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain male\|genotype:arid1b heterozygous	GSM8020223	GSM8020223: arid1b adult rep8; Danio rerio; RNA Seq	GSM8020223 r1	GSM8020223	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set2-het_A1_S13_R1_001.fastq.gz	fastq	2692714540.0	26660540.0	GSM8020223 r1	0:101	A:739519019;C:619307370;G:594887957;T:738995900;N:4294	101		739519019	619307370	594887957	738995900	4294	SRX23261715	SRS20163679	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29941	29941	SRR27592966	SRX23261714	SRS20163680	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep7	GSM8020222		source name:single dissected adult brain female\|tissue:single dissected adult brain female\|genotype:arid1b homozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep7	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain female		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain female\|genotype:arid1b homozygous	GSM8020222	GSM8020222: arid1b adult rep7; Danio rerio; RNA Seq	GSM8020222 r1	GSM8020222	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set1-hom_8_S38_R1_001.fastq.gz	fastq	3385303153.0	33517853.0	GSM8020222 r1	0:101	A:922612734;C:831122592;G:725118400;T:906435529;N:13898	101		922612734	831122592	725118400	906435529	13898	SRX23261714	SRS20163680	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29942	29942	SRR27592967	SRX23261713	SRS20163678	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep6	GSM8020221		source name:single dissected adult brain female\|tissue:single dissected adult brain female\|genotype:arid1b homozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep6	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain female		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain female\|genotype:arid1b homozygous	GSM8020221	GSM8020221: arid1b adult rep6; Danio rerio; RNA Seq	GSM8020221 r1	GSM8020221	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set1-hom_6_S36_R1_001.fastq.gz	fastq	4453651055.0	44095555.0	GSM8020221 r1	0:101	A:1190308155;C:1078598974;G:1012348343;T:1172377706;N:17877	101		1190308155	1078598974	1012348343	1172377706	17877	SRX23261713	SRS20163678	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29943	29943	SRR27592968	SRX23261712	SRS20163677	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep5	GSM8020220		source name:single dissected adult brain female\|tissue:single dissected adult brain female\|genotype:arid1b homozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep5	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain female		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain female\|genotype:arid1b homozygous	GSM8020220	GSM8020220: arid1b adult rep5; Danio rerio; RNA Seq	GSM8020220 r1	GSM8020220	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set1-hom_5_S35_R1_001.fastq.gz	fastq	3607941998.0	35722198.0	GSM8020220 r1	0:101	A:986679637;C:834475298;G:801712371;T:985059988;N:14704	101		986679637	834475298	801712371	985059988	14704	SRX23261712	SRS20163677	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29944	29944	SRR27592969	SRX23261711	SRS20163675	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep4	GSM8020219		source name:single dissected adult brain female\|tissue:single dissected adult brain female\|genotype:arid1b heterozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep4	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain female		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain female\|genotype:arid1b heterozygous	GSM8020219	GSM8020219: arid1b adult rep4; Danio rerio; RNA Seq	GSM8020219 r1	GSM8020219	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set1-het_4_S34_R1_001.fastq.gz	fastq	3406563249.0	33728349.0	GSM8020219 r1	0:101	A:929693102;C:825436822;G:742465339;T:908956167;N:11819	101		929693102	825436822	742465339	908956167	11819	SRX23261711	SRS20163675	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29945	29945	SRR27592970	SRX23261710	SRS20163676	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep3	GSM8020218		source name:single dissected adult brain female\|tissue:single dissected adult brain female\|genotype:arid1b heterozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep3	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain female		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain female\|genotype:arid1b heterozygous	GSM8020218	GSM8020218: arid1b adult rep3; Danio rerio; RNA Seq	GSM8020218 r1	GSM8020218	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set1-het_3_S33_R1_001.fastq.gz	fastq	3437288459.0	34032559.0	GSM8020218 r1	0:101	A:936275875;C:807195445;G:746272516;T:947530775;N:13848	101		936275875	807195445	746272516	947530775	13848	SRX23261710	SRS20163676	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29946	29946	SRR27592971	SRX23261709	SRS20163674	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep2	GSM8020217		source name:single dissected adult brain female\|tissue:single dissected adult brain female\|genotype:arid1b heterozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep2	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain female		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain female\|genotype:arid1b heterozygous	GSM8020217	GSM8020217: arid1b adult rep2; Danio rerio; RNA Seq	GSM8020217 r1	GSM8020217	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set1-het_2_S32_R1_001.fastq.gz	fastq	3033976067.0	30039367.0	GSM8020217 r1	0:101	A:813028951;C:730788577;G:668973332;T:821173824;N:11383	101		813028951	730788577	668973332	821173824	11383	SRX23261709	SRS20163674	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
29971	29971	SRR27592996	SRX23261684	SRS20163649	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.				arid1b adult rep1	GSM8020216		source name:single dissected adult brain female\|tissue:single dissected adult brain female\|genotype:arid1b heterozygous\|geo loc name:missing\|collection date:missing	arid1b adult rep1	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	single dissected adult brain female		RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		tissue:single dissected adult brain female\|genotype:arid1b heterozygous	GSM8020216	GSM8020216: arid1b adult rep1; Danio rerio; RNA Seq	GSM8020216 r1	GSM8020216	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		loader:fastq load.py	arid1b-adult-set1-het_1_S31_R1_001.fastq.gz	fastq	2831462785.0	28034285.0	GSM8020216 r1	0:101	A:770779666;C:662406160;G:622932995;T:775332651;N:11313	101		770779666	662406160	622932995	775332651	11313	SRX23261684	SRS20163649	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Adult	Adult	Brain	Nervous System
34554	34554	SRR32104359	SRX27449951	SRS23876473	SRP559533	PRJNA1214751	Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]	GSE287815	Transcriptome Analysis	During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.				17hpf Negative CNC 3	GSM8751784		source name:non neural crest from midbrain hindbrain boundary to somite 6\|tissue:non neural crest from midbrain hindbrain boundary to somite 6\|cell type:non neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry \|geo loc name:missing\|collection date:missing	17hpf Negative CNC 3	Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples	non neural crest from midbrain hindbrain boundary to somite 6		mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		tissue:non neural crest from midbrain hindbrain boundary to somite 6\|cell type:non neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry	GSM8751784	GSM8751784: 17hpf Negative CNC 3; Danio rerio; RNA Seq	GSM8751784 r1	GSM8751784	1	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP559533			Sox10_neg_17hpf_CNC_3_22029_combined_filtered.fastq.gz	fastq	6549316700.0	65493167.0	GSM8751784 r1	0:100	A:1904137226;C:1372226751;G:1395882591;T:1876995541;N:74591	100		1904137226	1372226751	1395882591	1876995541	74591	SRX27449951	SRS23876473	SRA2058978	Martik Lab, Molecular and Cell Biology, University of California Berkeley	Martik Lab, Molecular and Cell Biology, University of California Berkeley							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2025-01-23	Segmentation	Embryo	Brain	Nervous System
34555	34555	SRR32104360	SRX27449950	SRS23876471	SRP559533	PRJNA1214751	Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]	GSE287815	Transcriptome Analysis	During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.				17hpf Negative CNC 2	GSM8751783		source name:non neural crest from midbrain hindbrain boundary to somite 6\|tissue:non neural crest from midbrain hindbrain boundary to somite 6\|cell type:non neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry \|geo loc name:missing\|collection date:missing	17hpf Negative CNC 2	Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples	non neural crest from midbrain hindbrain boundary to somite 6		mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		tissue:non neural crest from midbrain hindbrain boundary to somite 6\|cell type:non neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry	GSM8751783	GSM8751783: 17hpf Negative CNC 2; Danio rerio; RNA Seq	GSM8751783 r1	GSM8751783	1	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP559533			Sox10_neg_17hpf_CNC_2_21339_combined_filtered.fastq.gz	fastq	2595442300.0	51908846.0	GSM8751783 r1	0:50	A:735396784;C:561568693;G:572114011;T:726356371;N:6441	50		735396784	561568693	572114011	726356371	6441	SRX27449950	SRS23876471	SRA2058978	Martik Lab, Molecular and Cell Biology, University of California Berkeley	Martik Lab, Molecular and Cell Biology, University of California Berkeley							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2025-01-23	Segmentation	Embryo	Brain	Nervous System
34556	34556	SRR32104361	SRX27449949	SRS23876470	SRP559533	PRJNA1214751	Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]	GSE287815	Transcriptome Analysis	During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.				17hpf Negative CNC 1	GSM8751782		source name:non neural crest from midbrain hindbrain boundary to somite 6\|tissue:non neural crest from midbrain hindbrain boundary to somite 6\|cell type:non neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry \|geo loc name:missing\|collection date:missing	17hpf Negative CNC 1	Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples	non neural crest from midbrain hindbrain boundary to somite 6		mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		tissue:non neural crest from midbrain hindbrain boundary to somite 6\|cell type:non neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry	GSM8751782	GSM8751782: 17hpf Negative CNC 1; Danio rerio; RNA Seq	GSM8751782 r1	GSM8751782	1	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP559533			Sox10_neg_17hpf_CNC_1_21310_combined_filtered.fastq.gz	fastq	2554400850.0	51088017.0	GSM8751782 r1	0:50	A:739730182;C:537827580;G:551508245;T:725296198;N:38645	50		739730182	537827580	551508245	725296198	38645	SRX27449949	SRS23876470	SRA2058978	Martik Lab, Molecular and Cell Biology, University of California Berkeley	Martik Lab, Molecular and Cell Biology, University of California Berkeley							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2025-01-23	Segmentation	Embryo	Brain	Nervous System
66168	66168	SRR15931293	SRX12221404	SRS10197471	SRP337626	PRJNA764215	Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]	GSE184359	Transcriptome Analysis	Individuals with mutations in CHD8 present with gastrointestinal complaints yet the underlying mechanisms are understudied. Here utilizing a stable constitutive chd8 mutant zebrafish model we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs enteric neural and glial progenitors emigrating from the neural tube and that their early migration capability was altered. At later stages although the intestinal colonization by the NCCs was complete we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons suggesting an intestinal hyposerotonemia in absence of chd8. Further transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8 NCC development intestinal homeostasis and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.	parent bioproject:PRJNA764218	pubmed:36375841		chd8+/+ 4dpf eNCC #1	GSM5585062		tissue:enteric Neural Crest Cells\|genotype:chd8 +/+	chd8+/+ 4dpf eNCC #1	Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.	enteric Neural Crest Cells		chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.		genotype:chd8 +/+	GSM5585062	GSM5585062: chd8+/+ 4dpf eNCC #1; Danio rerio; RNA Seq	GSM5585062		1	chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.	GEO Accession:GSM5585062	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP337626		loader:fastq load.py	GLHT1.fastq.gz	fastq	2075182700.0	41503654.0	GSM5585062 r1	0:50	A:596606751;C:434020268;G:443333228;T:601159724;N:62729	50		596606751	434020268	443333228	601159724	62729	SRX12221404	SRS10197471	SRA1296090	GEO	IGBMC	1	0.8763	0.23634	0.7349	0.56679	50	B	usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	France	2021-09-17	Larval	Larval	Brain	Nervous System
66169	66169	SRR15931300	SRX12221403	SRS10197470	SRP337626	PRJNA764215	Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]	GSE184359	Transcriptome Analysis	Individuals with mutations in CHD8 present with gastrointestinal complaints yet the underlying mechanisms are understudied. Here utilizing a stable constitutive chd8 mutant zebrafish model we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs enteric neural and glial progenitors emigrating from the neural tube and that their early migration capability was altered. At later stages although the intestinal colonization by the NCCs was complete we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons suggesting an intestinal hyposerotonemia in absence of chd8. Further transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8 NCC development intestinal homeostasis and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.	parent bioproject:PRJNA764218	pubmed:36375841		chd8+/ 4dpf eNCC #4	GSM5585069		tissue:enteric Neural Crest Cells\|genotype:chd8+/	chd8+/ 4dpf eNCC #4	Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.	enteric Neural Crest Cells		chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.		genotype:chd8+/	GSM5585069	GSM5585069: chd8+/ 4dpf eNCC #4; Danio rerio; RNA Seq	GSM5585069		1	chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.	GEO Accession:GSM5585069	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP337626		loader:fastq load.py	GLHT8.fastq.gz	fastq	2166642350.0	43332847.0	GSM5585069 r1	0:50	A:605269250;C:463067293;G:474978141;T:623262976;N:64690	50		605269250	463067293	474978141	623262976	64690	SRX12221403	SRS10197470	SRA1296090	GEO	IGBMC	1	0.87709	0.18108	0.73091	0.55465	50	B	usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	France	2021-09-17	Larval	Larval	Brain	Nervous System
66170	66170	SRR15931299	SRX12221402	SRS10197468	SRP337626	PRJNA764215	Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]	GSE184359	Transcriptome Analysis	Individuals with mutations in CHD8 present with gastrointestinal complaints yet the underlying mechanisms are understudied. Here utilizing a stable constitutive chd8 mutant zebrafish model we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs enteric neural and glial progenitors emigrating from the neural tube and that their early migration capability was altered. At later stages although the intestinal colonization by the NCCs was complete we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons suggesting an intestinal hyposerotonemia in absence of chd8. Further transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8 NCC development intestinal homeostasis and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.	parent bioproject:PRJNA764218	pubmed:36375841		chd8+/ 4dpf eNCC #3	GSM5585068		tissue:enteric Neural Crest Cells\|genotype:chd8+/	chd8+/ 4dpf eNCC #3	Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.	enteric Neural Crest Cells		chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.		genotype:chd8+/	GSM5585068	GSM5585068: chd8+/ 4dpf eNCC #3; Danio rerio; RNA Seq	GSM5585068		1	chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.	GEO Accession:GSM5585068	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP337626		loader:fastq load.py	GLHT7.fastq.gz	fastq	2044848000.0	40896960.0	GSM5585068 r1	0:50	A:570340694;C:448773695;G:458077948;T:567595155;N:60508	50		570340694	448773695	458077948	567595155	60508	SRX12221402	SRS10197468	SRA1296090	GEO	IGBMC	1	0.89989	0.13688	0.74761	0.51955	50	B	usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	France	2021-09-17	Larval	Larval	Brain	Nervous System
66171	66171	SRR15931298	SRX12221401	SRS10197467	SRP337626	PRJNA764215	Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]	GSE184359	Transcriptome Analysis	Individuals with mutations in CHD8 present with gastrointestinal complaints yet the underlying mechanisms are understudied. Here utilizing a stable constitutive chd8 mutant zebrafish model we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs enteric neural and glial progenitors emigrating from the neural tube and that their early migration capability was altered. At later stages although the intestinal colonization by the NCCs was complete we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons suggesting an intestinal hyposerotonemia in absence of chd8. Further transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8 NCC development intestinal homeostasis and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.	parent bioproject:PRJNA764218	pubmed:36375841		chd8+/ 4dpf eNCC #2	GSM5585067		tissue:enteric Neural Crest Cells\|genotype:chd8+/	chd8+/ 4dpf eNCC #2	Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.	enteric Neural Crest Cells		chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.		genotype:chd8+/	GSM5585067	GSM5585067: chd8+/ 4dpf eNCC #2; Danio rerio; RNA Seq	GSM5585067		1	chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.	GEO Accession:GSM5585067	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP337626		loader:fastq load.py	GLHT6.fastq.gz	fastq	2236566700.0	44731334.0	GSM5585067 r1	0:50	A:632520025;C:482922105;G:493836270;T:627225283;N:63017	50		632520025	482922105	493836270	627225283	63017	SRX12221401	SRS10197467	SRA1296090	GEO	IGBMC	1	0.87472	0.13005	0.73214	0.54467	50	B	usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	France	2021-09-17	Larval	Larval	Brain	Nervous System
66172	66172	SRR15931297	SRX12221400	SRS10197469	SRP337626	PRJNA764215	Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]	GSE184359	Transcriptome Analysis	Individuals with mutations in CHD8 present with gastrointestinal complaints yet the underlying mechanisms are understudied. Here utilizing a stable constitutive chd8 mutant zebrafish model we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs enteric neural and glial progenitors emigrating from the neural tube and that their early migration capability was altered. At later stages although the intestinal colonization by the NCCs was complete we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons suggesting an intestinal hyposerotonemia in absence of chd8. Further transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8 NCC development intestinal homeostasis and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.	parent bioproject:PRJNA764218	pubmed:36375841		chd8+/ 4dpf eNCC #1	GSM5585066		tissue:enteric Neural Crest Cells\|genotype:chd8+/	chd8+/ 4dpf eNCC #1	Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.	enteric Neural Crest Cells		chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.		genotype:chd8+/	GSM5585066	GSM5585066: chd8+/ 4dpf eNCC #1; Danio rerio; RNA Seq	GSM5585066		1	chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.	GEO Accession:GSM5585066	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP337626		loader:fastq load.py	GLHT5.fastq.gz	fastq	2445365700.0	48907314.0	GSM5585066 r1	0:50	A:652878336;C:569347668;G:578346047;T:644721788;N:71861	50		652878336	569347668	578346047	644721788	71861	SRX12221400	SRS10197469	SRA1296090	GEO	IGBMC	1	0.91958	0.08571	0.72222	0.51361	50	B	usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	France	2021-09-17	Larval	Larval	Brain	Nervous System
66173	66173	SRR15931296	SRX12221399	SRS10197466	SRP337626	PRJNA764215	Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]	GSE184359	Transcriptome Analysis	Individuals with mutations in CHD8 present with gastrointestinal complaints yet the underlying mechanisms are understudied. Here utilizing a stable constitutive chd8 mutant zebrafish model we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs enteric neural and glial progenitors emigrating from the neural tube and that their early migration capability was altered. At later stages although the intestinal colonization by the NCCs was complete we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons suggesting an intestinal hyposerotonemia in absence of chd8. Further transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8 NCC development intestinal homeostasis and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.	parent bioproject:PRJNA764218	pubmed:36375841		chd8+/+ 4dpf eNCC #4	GSM5585065		tissue:enteric Neural Crest Cells\|genotype:chd8 +/+	chd8+/+ 4dpf eNCC #4	Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.	enteric Neural Crest Cells		chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.		genotype:chd8 +/+	GSM5585065	GSM5585065: chd8+/+ 4dpf eNCC #4; Danio rerio; RNA Seq	GSM5585065		1	chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.	GEO Accession:GSM5585065	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP337626		loader:fastq load.py	GLHT4.fastq.gz	fastq	2016451500.0	40329030.0	GSM5585065 r1	0:50	A:554611579;C:447165784;G:458213114;T:556400342;N:60681	50		554611579	447165784	458213114	556400342	60681	SRX12221399	SRS10197466	SRA1296090	GEO	IGBMC	1	0.89742	0.11584	0.72127	0.52068	50	B	usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	France	2021-09-17	Larval	Larval	Brain	Nervous System
66174	66174	SRR15931295	SRX12221398	SRS10197465	SRP337626	PRJNA764215	Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]	GSE184359	Transcriptome Analysis	Individuals with mutations in CHD8 present with gastrointestinal complaints yet the underlying mechanisms are understudied. Here utilizing a stable constitutive chd8 mutant zebrafish model we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs enteric neural and glial progenitors emigrating from the neural tube and that their early migration capability was altered. At later stages although the intestinal colonization by the NCCs was complete we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons suggesting an intestinal hyposerotonemia in absence of chd8. Further transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8 NCC development intestinal homeostasis and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.	parent bioproject:PRJNA764218	pubmed:36375841		chd8+/+ 4dpf eNCC #3	GSM5585064		tissue:enteric Neural Crest Cells\|genotype:chd8 +/+	chd8+/+ 4dpf eNCC #3	Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.	enteric Neural Crest Cells		chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.		genotype:chd8 +/+	GSM5585064	GSM5585064: chd8+/+ 4dpf eNCC #3; Danio rerio; RNA Seq	GSM5585064		1	chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.	GEO Accession:GSM5585064	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP337626		loader:fastq load.py	GLHT3.fastq.gz	fastq	2081908800.0	41638176.0	GSM5585064 r1	0:50	A:583234858;C:447061909;G:457587573;T:593962758;N:61702	50		583234858	447061909	457587573	593962758	61702	SRX12221398	SRS10197465	SRA1296090	GEO	IGBMC	1	0.88033	0.16506	0.75138	0.50655	50	B	usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	France	2021-09-17	Larval	Larval	Brain	Nervous System
66175	66175	SRR15931294	SRX12221397	SRS10197464	SRP337626	PRJNA764215	Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]	GSE184359	Transcriptome Analysis	Individuals with mutations in CHD8 present with gastrointestinal complaints yet the underlying mechanisms are understudied. Here utilizing a stable constitutive chd8 mutant zebrafish model we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs enteric neural and glial progenitors emigrating from the neural tube and that their early migration capability was altered. At later stages although the intestinal colonization by the NCCs was complete we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons suggesting an intestinal hyposerotonemia in absence of chd8. Further transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8 NCC development intestinal homeostasis and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.	parent bioproject:PRJNA764218	pubmed:36375841		chd8+/+ 4dpf eNCC #2	GSM5585063		tissue:enteric Neural Crest Cells\|genotype:chd8 +/+	chd8+/+ 4dpf eNCC #2	Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.	enteric Neural Crest Cells		chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.		genotype:chd8 +/+	GSM5585063	GSM5585063: chd8+/+ 4dpf eNCC #2; Danio rerio; RNA Seq	GSM5585063		1	chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. At 4 dpf dpf the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma ref 59417C 100ML. The digestion was stopped post 10 minutes by adding 50 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl of FACS Max medium the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm. We stored the GFP positive cells at 80 °C in 10 µl of PBS RNAsine 1 U/µl. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe Saint Germain en Laye France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina San Diego CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter Villepinte France the size and concentration of libraries were assessed by capillary electrophoresis.	GEO Accession:GSM5585063	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP337626		loader:fastq load.py	GLHT2.fastq.gz	fastq	2151869900.0	43037398.0	GSM5585063 r1	0:50	A:581790111;C:491684308;G:500076074;T:578254560;N:64847	50		581790111	491684308	500076074	578254560	64847	SRX12221397	SRS10197464	SRA1296090	GEO	IGBMC	1	0.915	0.08656	0.72537	0.52001	50	B	usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	France	2021-09-17	Larval	Larval	Brain	Nervous System
75652	75652	SRR24758212	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_A01.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	196502541.0	3852991.0	GSM7432137 r1	0:51	A:49165276;C:47981089;G:48399038;T:50940008;N:17130	51		49165276	47981089	48399038	50940008	17130	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.72705	0.06867	0.88552	0.54207	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75653	75653	SRR24758213	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_A10.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	57801819.0	1133369.0	GSM7432137 r10	0:51	A:15530697;C:12658068;G:12843873;T:16764026;N:5155	51		15530697	12658068	12843873	16764026	5155	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.63663	0.42833	0.92111	0.57817	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75654	75654	SRR24758214	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_A11.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	72272559.0	1417109.0	GSM7432137 r11	0:51	A:18233220;C:16632293;G:17042518;T:20358144;N:6384	51		18233220	16632293	17042518	20358144	6384	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.67945	0.12353	0.94095	0.48607	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75655	75655	SRR24758215	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_A12.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	187811019.0	3682569.0	GSM7432137 r12	0:51	A:49325726;C:43713702;G:44241940;T:50513058;N:16593	51		49325726	43713702	44241940	50513058	16593	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.84473	0.12213	0.90666	0.56528	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75656	75656	SRR24758216	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B01.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	24050070.0	471570.0	GSM7432137 r13	0:51	A:5907474;C:6114990;G:5982982;T:6042494;N:2130	51		5907474	6114990	5982982	6042494	2130	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.47163	0.30199	0.93933	0.53872	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75657	75657	SRR24758217	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B02.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	275774544.0	5407344.0	GSM7432137 r14	0:51	A:69654405;C:67726837;G:68298856;T:70070552;N:23894	51		69654405	67726837	68298856	70070552	23894	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.84442	0.07023	0.88923	0.53422	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75658	75658	SRR24758218	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B03.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	226648335.0	4444085.0	GSM7432137 r15	0:51	A:57531232;C:54256013;G:54956617;T:59884654;N:19819	51		57531232	54256013	54956617	59884654	19819	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.80693	0.10694	0.9179	0.52785	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75659	75659	SRR24758219	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B04.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	247590159.0	4854709.0	GSM7432137 r16	0:51	A:64151909;C:59176102;G:59606872;T:64633924;N:21352	51		64151909	59176102	59606872	64633924	21352	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.85951	0.0727	0.88598	0.52101	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75660	75660	SRR24758220	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B05.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	236963799.0	4646349.0	GSM7432137 r17	0:51	A:61256843;C:56596118;G:57122766;T:61967590;N:20482	51		61256843	56596118	57122766	61967590	20482	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.86507	0.0857	0.89556	0.38852	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75661	75661	SRR24758221	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B06.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	174345642.0	3418542.0	GSM7432137 r18	0:51	A:43218316;C:42711053;G:43771526;T:44629449;N:15298	51		43218316	42711053	43771526	44629449	15298	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.85865	0.02991	0.91167	0.40975	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75662	75662	SRR24758222	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B07.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	310253298.0	6083398.0	GSM7432137 r19	0:51	A:79341090;C:74303124;G:75662036;T:80919848;N:27200	51		79341090	74303124	75662036	80919848	27200	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.87708	0.0717	0.89727	0.46207	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75663	75663	SRR24758223	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_A02.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	566253.0	11103.0	GSM7432137 r2	0:51	A:136988;C:128378;G:125521;T:175317;N:49	51		136988	128378	125521	175317	49	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.67766	0.11307	0.95172	0.5382	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75664	75664	SRR24758224	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B08.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	346341.0	6791.0	GSM7432137 r20	0:51	A:84780;C:84123;G:83720;T:93689;N:29	51		84780	84123	83720	93689	29	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.63515	0.09273	0.96802	0.52162	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75665	75665	SRR24758225	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B09.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	377961.0	7411.0	GSM7432137 r21	0:51	A:95293;C:90257;G:87563;T:104807;N:41	51		95293	90257	87563	104807	41	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.69105	0.08086	0.96455	0.53115	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75666	75666	SRR24758226	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B10.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	2250936.0	44136.0	GSM7432137 r22	0:51	A:539924;C:650712;G:518629;T:541473;N:198	51		539924	650712	518629	541473	198	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.27445	0.04803	0.95276	0.53885	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75667	75667	SRR24758227	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B11.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	207937659.0	4077209.0	GSM7432137 r23	0:51	A:52800304;C:49954044;G:50494891;T:54670231;N:18189	51		52800304	49954044	50494891	54670231	18189	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.83348	0.06056	0.87643	0.52466	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75668	75668	SRR24758228	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_B12.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	116941317.0	2292967.0	GSM7432137 r24	0:51	A:31454818;C:25883611;G:26279868;T:33312749;N:10271	51		31454818	25883611	26279868	33312749	10271	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.76622	0.21094	0.92413	0.55894	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75669	75669	SRR24758229	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_C01.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	539172.0	10572.0	GSM7432137 r25	0:51	A:134771;C:127049;G:127559;T:149745;N:48	51		134771	127049	127559	149745	48	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.74289	0.09475	0.94769	0.55262	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75670	75670	SRR24758230	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_C02.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	249154176.0	4885376.0	GSM7432137 r26	0:51	A:62840979;C:61240493;G:61835852;T:63215177;N:21675	51		62840979	61240493	61835852	63215177	21675	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.89326	0.07803	0.84967	0.51569	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75671	75671	SRR24758231	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_C03.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	641019.0	12569.0	GSM7432137 r27	0:51	A:175739;C:156164;G:141289;T:167772;N:55	51		175739	156164	141289	167772	55	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.50169	0.06287	0.95611	0.57318	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75672	75672	SRR24758232	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_C04.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	223399839.0	4380389.0	GSM7432137 r28	0:51	A:58104465;C:53189406;G:53552668;T:58534071;N:19229	51		58104465	53189406	53552668	58534071	19229	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.84775	0.07316	0.89883	0.53245	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75673	75673	SRR24758233	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_C05.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	2148528.0	42128.0	GSM7432137 r29	0:51	A:456160;C:713081;G:433891;T:545183;N:213	51		456160	713081	433891	545183	213	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.31226	0.04264	0.94718	0.54464	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75674	75674	SRR24758234	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_A03.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	182987337.0	3587987.0	GSM7432137 r3	0:51	A:48471316;C:41287723;G:41835653;T:51376450;N:16195	51		48471316	41287723	41835653	51376450	16195	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.79625	0.12945	0.87042	0.54466	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75675	75675	SRR24758235	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_C06.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	277189131.0	5435081.0	GSM7432137 r30	0:51	A:72722594;C:65268944;G:65970657;T:73202676;N:24260	51		72722594	65268944	65970657	73202676	24260	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.85793	0.09135	0.89428	0.53659	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75676	75676	SRR24758236	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_C07.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	51855423.0	1016773.0	GSM7432137 r31	0:51	A:12581543;C:12652880;G:12719547;T:13896926;N:4527	51		12581543	12652880	12719547	13896926	4527	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.64717	0.1549	0.93042	0.59143	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System
75677	75677	SRR24758237	SRX20534082	SRS17842609	SRP440051	PRJNA977246	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233662	Transcriptome Analysis	Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model we reveal a molecular mechanism for brain specific angiogenesis that operates under the control of Wnt7a/b ligands well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition the Wnt/ß catenin dependent organotypic control of brain angiogenesis is lost resulting in properly patterned yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism sheds light on tip cell mechanistic angiodiversity and thereby illustrates how organs by imposing local constraints on angiogenic tip cells can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		source name:Brain\|tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino\|geo loc name:missing\|collection date:missing	Photoconverted brain endothelial cells rep2	Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files with every column a cell and every row a gene.	Brain	Morpholino injection	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2	Standard	tissue:Brain\|age:30 hpf\|cell type:Endothelial cells\|genotype:Tgfli1a:Gal4FF;UAS:Kaede\|treatment:WT and gpr124 morpholino	GSM7432137	GSM7432137: Photoconverted brain endothelial cells rep2; Danio rerio; RNA Seq	GSM7432137 r1	GSM7432137	1	Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss objective lenses: Plan Apochromat ×20/0.8 M27. Briefly anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min in TrypLE select Thermo Fischer Scientific 12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS filtered and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 – 26 cycles. post bead purification overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC the cDNA was fragmented and tagged tagmented using Tn5 transposase and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina using dual indexing and 50 base read length. ScRNA Seq with Smart seq2		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP440051		loader:fastq load.py	GC049751_C08.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	196417422.0	3851322.0	GSM7432137 r32	0:51	A:49916233;C:47717459;G:48374054;T:50392337;N:17339	51		49916233	47717459	48374054	50392337	17339	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.75845	0.10284	0.91001	0.55748	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Sweden	2023-05-29	Pharyngula	Embryo	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");;