metadata: run_metadata: 1,918 rows where experiment.library_strategy = "RNA-Seq", technology = "smartseq" and tissue

1,918 rows where experiment.library_strategy = "RNA-Seq", 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.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.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.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
30276	30276	SRR27747452	SRX23412768	SRS20268089	SRP486175	PRJNA1069777	Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish bulk RNA Seq	GSE254345	Transcriptome Analysis	Sensorimotor reflex circuits engage distinct neuronal subtypes defined by precise connectivity to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a / mutants and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed each generating two samples phox2a / and sibling control. Bulk RNA sequencing was performed.				Hindbrain vestibular neurons phox2a / replicate 4	GSM8038036		tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a / \|geo loc name:missing\|collection date:missing	Hindbrain vestibular neurons phox2a / replicate 4	DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample	Hindbrain vestibular neurons	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara	time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a /	GSM8038036	GSM8038036: Hindbrain vestibular neurons phox2a / replicate 4; Danio rerio; RNA Seq	GSM8038036 r1	GSM8038036	1	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486175		loader:fastq load.py	1209_phox2a_S31_L002_R1_001.fastq.gz 1209_phox2a_S31_L002_R2_001.fastq.gz	fastq fastq	4002287934.0	39238117.0	GSM8038036 r1	0:51 1:51	A:1128557040;C:810913651;G:820439585;T:1242297099;N:80559	51	51	1128557040	810913651	820439585	1242297099	80559	SRX23412768	SRS20268089	SRA1792521	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2024-01-26	Larval	Larval	Brain	Nervous System
30277	30277	SRR27747453	SRX23412767	SRS20268088	SRP486175	PRJNA1069777	Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish bulk RNA Seq	GSE254345	Transcriptome Analysis	Sensorimotor reflex circuits engage distinct neuronal subtypes defined by precise connectivity to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a / mutants and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed each generating two samples phox2a / and sibling control. Bulk RNA sequencing was performed.				Hindbrain vestibular neurons siblings replicate 4	GSM8038035		tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/ \|geo loc name:missing\|collection date:missing	Hindbrain vestibular neurons siblings replicate 4	DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample	Hindbrain vestibular neurons	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara	time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/	GSM8038035	GSM8038035: Hindbrain vestibular neurons siblings replicate 4; Danio rerio; RNA Seq	GSM8038035 r1	GSM8038035	1	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486175		loader:fastq load.py	1209_siblings_S32_L002_R1_001.fastq.gz 1209_siblings_S32_L002_R2_001.fastq.gz	fastq fastq	4533715686.0	44448193.0	GSM8038035 r1	0:51 1:51	A:1331986982;C:918253301;G:901739294;T:1381651915;N:84194	51	51	1331986982	918253301	901739294	1381651915	84194	SRX23412767	SRS20268088	SRA1792521	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2024-01-26	Larval	Larval	Brain	Nervous System
30278	30278	SRR27747454	SRX23412766	SRS20268087	SRP486175	PRJNA1069777	Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish bulk RNA Seq	GSE254345	Transcriptome Analysis	Sensorimotor reflex circuits engage distinct neuronal subtypes defined by precise connectivity to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a / mutants and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed each generating two samples phox2a / and sibling control. Bulk RNA sequencing was performed.				Hindbrain vestibular neurons phox2a / replicate 3	GSM8038034		tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a / \|geo loc name:missing\|collection date:missing	Hindbrain vestibular neurons phox2a / replicate 3	DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample	Hindbrain vestibular neurons	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara	time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a /	GSM8038034	GSM8038034: Hindbrain vestibular neurons phox2a / replicate 3; Danio rerio; RNA Seq	GSM8038034 r1	GSM8038034	1	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486175		loader:fastq load.py	1201_phox2a_S29_L002_R1_001.fastq.gz 1201_phox2a_S29_L002_R2_001.fastq.gz	fastq fastq	6231969582.0	61097741.0	GSM8038034 r1	0:51 1:51	A:1936318076;C:1131055224;G:1080268483;T:2084206449;N:121350	51	51	1936318076	1131055224	1080268483	2084206449	121350	SRX23412766	SRS20268087	SRA1792521	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2024-01-26	Larval	Larval	Brain	Nervous System
30279	30279	SRR27747455	SRX23412765	SRS20268084	SRP486175	PRJNA1069777	Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish bulk RNA Seq	GSE254345	Transcriptome Analysis	Sensorimotor reflex circuits engage distinct neuronal subtypes defined by precise connectivity to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a / mutants and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed each generating two samples phox2a / and sibling control. Bulk RNA sequencing was performed.				Hindbrain vestibular neurons siblings replicate 3	GSM8038033		tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/ \|geo loc name:missing\|collection date:missing	Hindbrain vestibular neurons siblings replicate 3	DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample	Hindbrain vestibular neurons	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara	time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/	GSM8038033	GSM8038033: Hindbrain vestibular neurons siblings replicate 3; Danio rerio; RNA Seq	GSM8038033 r1	GSM8038033	1	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486175		loader:fastq load.py	1201_siblings_S30_L002_R1_001.fastq.gz 1201_siblings_S30_L002_R2_001.fastq.gz	fastq fastq	3665201598.0	35933349.0	GSM8038033 r1	0:51 1:51	A:1089767593;C:738549860;G:726974766;T:1109839399;N:69980	51	51	1089767593	738549860	726974766	1109839399	69980	SRX23412765	SRS20268084	SRA1792521	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2024-01-26	Larval	Larval	Brain	Nervous System
30280	30280	SRR27747456	SRX23412764	SRS20268085	SRP486175	PRJNA1069777	Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish bulk RNA Seq	GSE254345	Transcriptome Analysis	Sensorimotor reflex circuits engage distinct neuronal subtypes defined by precise connectivity to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a / mutants and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed each generating two samples phox2a / and sibling control. Bulk RNA sequencing was performed.				Hindbrain vestibular neurons phox2a / replicate 2	GSM8038032		tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a / \|geo loc name:missing\|collection date:missing	Hindbrain vestibular neurons phox2a / replicate 2	DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample	Hindbrain vestibular neurons	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara	time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a /	GSM8038032	GSM8038032: Hindbrain vestibular neurons phox2a / replicate 2; Danio rerio; RNA Seq	GSM8038032 r1	GSM8038032	1	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486175		loader:fastq load.py	1122_phox2a_S27_L002_R1_001.fastq.gz 1122_phox2a_S27_L002_R2_001.fastq.gz	fastq fastq	3449800956.0	33821578.0	GSM8038032 r1	0:51 1:51	A:1024161989;C:698197523;G:689509862;T:1037871222;N:60360	51	51	1024161989	698197523	689509862	1037871222	60360	SRX23412764	SRS20268085	SRA1792521	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2024-01-26	Larval	Larval	Brain	Nervous System
30281	30281	SRR27747457	SRX23412763	SRS20268086	SRP486175	PRJNA1069777	Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish bulk RNA Seq	GSE254345	Transcriptome Analysis	Sensorimotor reflex circuits engage distinct neuronal subtypes defined by precise connectivity to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a / mutants and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed each generating two samples phox2a / and sibling control. Bulk RNA sequencing was performed.				Hindbrain vestibular neurons siblings replicate 2	GSM8038031		tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/ \|geo loc name:missing\|collection date:missing	Hindbrain vestibular neurons siblings replicate 2	DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample	Hindbrain vestibular neurons	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara	time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/	GSM8038031	GSM8038031: Hindbrain vestibular neurons siblings replicate 2; Danio rerio; RNA Seq	GSM8038031 r1	GSM8038031	1	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486175		loader:fastq load.py	1122_siblings_S28_L002_R1_001.fastq.gz 1122_siblings_S28_L002_R2_001.fastq.gz	fastq fastq	3326329752.0	32611076.0	GSM8038031 r1	0:51 1:51	A:939623583;C:720094628;G:722500041;T:944060444;N:51056	51	51	939623583	720094628	722500041	944060444	51056	SRX23412763	SRS20268086	SRA1792521	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2024-01-26	Larval	Larval	Brain	Nervous System
30282	30282	SRR27747458	SRX23412762	SRS20268083	SRP486175	PRJNA1069777	Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish bulk RNA Seq	GSE254345	Transcriptome Analysis	Sensorimotor reflex circuits engage distinct neuronal subtypes defined by precise connectivity to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a / mutants and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed each generating two samples phox2a / and sibling control. Bulk RNA sequencing was performed.				Hindbrain vestibular neurons phox2a / replicate 1	GSM8038030		tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a / \|geo loc name:missing\|collection date:missing	Hindbrain vestibular neurons phox2a / replicate 1	DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample	Hindbrain vestibular neurons	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara	time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a /	GSM8038030	GSM8038030: Hindbrain vestibular neurons phox2a / replicate 1; Danio rerio; RNA Seq	GSM8038030 r1	GSM8038030	1	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486175		loader:fastq load.py	1019_phox2a_S25_L002_R1_001.fastq.gz 1019_phox2a_S25_L002_R2_001.fastq.gz	fastq fastq	3186783246.0	31242973.0	GSM8038030 r1	0:51 1:51	A:955687278;C:636490356;G:630374686;T:964170971;N:59955	51	51	955687278	636490356	630374686	964170971	59955	SRX23412762	SRS20268083	SRA1792521	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2024-01-26	Larval	Larval	Brain	Nervous System
30283	30283	SRR27747459	SRX23412761	SRS20268082	SRP486175	PRJNA1069777	Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish bulk RNA Seq	GSE254345	Transcriptome Analysis	Sensorimotor reflex circuits engage distinct neuronal subtypes defined by precise connectivity to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a / mutants and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed each generating two samples phox2a / and sibling control. Bulk RNA sequencing was performed.				Hindbrain vestibular neurons siblings replicate 1	GSM8038029		tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/ \|geo loc name:missing\|collection date:missing	Hindbrain vestibular neurons siblings replicate 1	DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample	Hindbrain vestibular neurons	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara	time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/	GSM8038029	GSM8038029: Hindbrain vestibular neurons siblings replicate 1; Danio rerio; RNA Seq	GSM8038029 r1	GSM8038029	1	RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486175		loader:fastq load.py	1019_siblings_S26_L002_R1_001.fastq.gz 1019_siblings_S26_L002_R2_001.fastq.gz	fastq fastq	3481817226.0	34135463.0	GSM8038029 r1	0:51 1:51	A:1015152374;C:724318215;G:717469149;T:1024812342;N:65146	51	51	1015152374	724318215	717469149	1024812342	65146	SRX23412761	SRS20268082	SRA1792521	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2024-01-26	Larval	Larval	Brain	Nervous System
33311	33311	SRR29927545	SRX25421505	SRS22081661	SRP521592	PRJNA1139127	Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration	PRJNA1139127	Other	Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.				ON 3d rep3	MCWR 2019 000157		strain:wild type\|dev stage:adult\|collection date:2019 10 18\|geo loc name:USA: Wisconsin Milwaukee\|sex:female\|tissue:optic nerve\|treatment:ON 3d rep3\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: 3 xxx post injury optic nerve	ON 3d rep3	ON 3d rep3	SMART Seqv4			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP521592			MCWR_2019_000157_S28_L001_R1_001.fastq.gz MCWR_2019_000157_S28_L001_R2_001.fastq.gz MCWR_2019_000157_S28_L002_R1_001.fastq.gz MCWR_2019_000157_S28_L002_R2_001.fastq.gz	fastq fastq fastq fastq	12637756180.0	41976869.0	MCWR 2019 000157 S28 L001 R1 001.fastq.gz	0:150.53 1:150.53	A:3303913534;C:3007130754;G:3036624621;T:3289934437;N:152834	150	150	3303913534	3007130754	3036624621	3289934437	152834	SRX25421505	SRS22081661	SRA1930690	Medical College of Wisconsin\|Cell Biology, Neurobiology, and Anatomy	Medical College of Wisconsin	2	0.9516	0.95161	0.06268	0.06324	0.7245	0.72539	0.50499	0.5082	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2024-07-23	Adult	Adult	Brain	Nervous System
33312	33312	SRR29927546	SRX25421504	SRS22081660	SRP521592	PRJNA1139127	Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration	PRJNA1139127	Other	Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.				ON 3d rep2	MCWR 2019 000156		strain:wild type\|dev stage:adult\|collection date:2019 10 18\|geo loc name:USA: Wisconsin Milwaukee\|sex:female\|tissue:optic nerve\|treatment:ON 3d rep2\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: 3 xxx post injury optic nerve	ON 3d rep2	ON 3d rep2	SMART Seqv4			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP521592			MCWR_2019_000156_S27_L001_R1_001.fastq.gz MCWR_2019_000156_S27_L001_R2_001.fastq.gz MCWR_2019_000156_S27_L002_R1_001.fastq.gz MCWR_2019_000156_S27_L002_R2_001.fastq.gz	fastq fastq fastq fastq	8225156065.0	27320970.0	MCWR 2019 000156 S27 L001 R1 001.fastq.gz	0:150.53 1:150.53	A:2177338510;C:1933476228;G:1950713017;T:2163526872;N:101438	150	150	2177338510	1933476228	1950713017	2163526872	101438	SRX25421504	SRS22081660	SRA1930690	Medical College of Wisconsin\|Cell Biology, Neurobiology, and Anatomy	Medical College of Wisconsin	2	0.94816	0.94656	0.06839	0.06869	0.71873	0.72099	0.52048	0.51823	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2024-07-23	Adult	Adult	Brain	Nervous System
33314	33314	SRR29927548	SRX25421502	SRS22081658	SRP521592	PRJNA1139127	Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration	PRJNA1139127	Other	Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.				ON 3d rep1	MCWR 2019 000149		strain:wild type\|dev stage:adult\|collection date:2019 10 18\|geo loc name:USA: Wisconsin Milwaukee\|sex:female\|tissue:optic nerve\|treatment:ON 3d rep1\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: 3 xxx post injury optic nerve	ON 3d rep1	ON 3d rep1	SMART Seqv4			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP521592			MCWR_2019_000149_S20_L001_R1_001.fastq.gz MCWR_2019_000149_S20_L001_R2_001.fastq.gz MCWR_2019_000149_S20_L002_R1_001.fastq.gz MCWR_2019_000149_S20_L002_R2_001.fastq.gz	fastq fastq fastq fastq	11234251579.0	37312508.0	MCWR 2019 000149 S20 L001 R1 001.fastq.gz	0:150.54 1:150.55	A:2884045359;C:2724366727;G:2744442031;T:2881252209;N:145253	150	150	2884045359	2724366727	2744442031	2881252209	145253	SRX25421502	SRS22081658	SRA1930690	Medical College of Wisconsin\|Cell Biology, Neurobiology, and Anatomy	Medical College of Wisconsin	2	0.95118	0.95151	0.09345	0.09458	0.69589	0.6953	0.47864	0.4794	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2024-07-23	Adult	Adult	Brain	Nervous System
33315	33315	SRR29927549	SRX25421501	SRS22081657	SRP521592	PRJNA1139127	Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration	PRJNA1139127	Other	Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.				ON Control rep3	MCWR 2019 000148		strain:wild type\|dev stage:adult\|collection date:2019 10 18\|geo loc name:USA: Wisconsin Milwaukee\|sex:female\|tissue:optic nerve\|treatment:ON Control rep3\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: naive optic nerve	ON Control rep3	ON Control rep3	SMART Seqv4			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP521592			MCWR_2019_000148_S19_L002_R2_001.fastq.gz MCWR_2019_000148_S19_L002_R1_001.fastq.gz MCWR_2019_000148_S19_L001_R2_001.fastq.gz MCWR_2019_000148_S19_L001_R1_001.fastq.gz	fastq fastq fastq fastq	10659326860.0	35402192.0	MCWR 2019 000148 S19 L001 R1 001.fastq.gz	0:150.55 1:150.55	A:2756153864;C:2571019186;G:2591020090;T:2740998974;N:134746	150	150	2756153864	2571019186	2591020090	2740998974	134746	SRX25421501	SRS22081657	SRA1930690	Medical College of Wisconsin\|Cell Biology, Neurobiology, and Anatomy	Medical College of Wisconsin	2	0.95167	0.95091	0.09159	0.09247	0.74852	0.74961	0.46451	0.46354	150	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2024-07-23	Adult	Adult	Brain	Nervous System
33316	33316	SRR29927550	SRX25421500	SRS22081656	SRP521592	PRJNA1139127	Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration	PRJNA1139127	Other	Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.				ON Control rep2	MCWR 2019 000147		strain:wild type\|dev stage:adult\|collection date:2019 10 18\|geo loc name:USA: Wisconsin Milwaukee\|sex:female\|tissue:optic nerve\|treatment:ON Control rep2\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: naive optic nerve	ON Control rep2	ON Control rep2	SMART Seqv4			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP521592			MCWR_2019_000147_S18_L002_R2_001.fastq.gz MCWR_2019_000147_S18_L002_R1_001.fastq.gz MCWR_2019_000147_S18_L001_R2_001.fastq.gz MCWR_2019_000147_S18_L001_R1_001.fastq.gz	fastq fastq fastq fastq	13568087444.0	45061061.0	MCWR 2019 000147 S18 L001 R1 001.fastq.gz	0:150.55 1:150.55	A:3431511167;C:3343690230;G:3365044224;T:3427668362;N:173461	150	150	3431511167	3343690230	3365044224	3427668362	173461	SRX25421500	SRS22081656	SRA1930690	Medical College of Wisconsin\|Cell Biology, Neurobiology, and Anatomy	Medical College of Wisconsin	2	0.95653	0.95547	0.08512	0.08497	0.73093	0.73143	0.46625	0.46899	150	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2024-07-23	Adult	Adult	Brain	Nervous System
33317	33317	SRR29927551	SRX25421499	SRS22081655	SRP521592	PRJNA1139127	Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration	PRJNA1139127	Other	Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.				ON Control rep1	MCWR 2019 000146		strain:wild type\|dev stage:adult\|collection date:2019 10 18\|geo loc name:USA: Wisconsin Milwaukee\|sex:female\|tissue:optic nerve\|treatment:ON Control rep1\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: naive optic nerve	ON Control rep1	ON Control rep1	SMART Seqv4			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP521592			MCWR_2019_000146_S17_L002_R2_001.fastq.gz MCWR_2019_000146_S17_L002_R1_001.fastq.gz MCWR_2019_000146_S17_L001_R2_001.fastq.gz MCWR_2019_000146_S17_L001_R1_001.fastq.gz	fastq fastq fastq fastq	10264964293.0	34089023.0	MCWR 2019 000146 S17 L001 R1 001.fastq.gz	0:150.56 1:150.56	A:2551033720;C:2573448189;G:2588121299;T:2552234053;N:127032	150	150	2551033720	2573448189	2588121299	2552234053	127032	SRX25421499	SRS22081655	SRA1930690	Medical College of Wisconsin\|Cell Biology, Neurobiology, and Anatomy	Medical College of Wisconsin	2	0.95724	0.95715	0.07005	0.07059	0.75637	0.75732	0.42392	0.41384	151	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2024-07-23	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
34925	34925	SRR32424865	SRX27754020	SRS24139551	SRP565442	PRJNA1226487	Separate brainstem circuits for fast steering and slow exploratory turns	GSE290157	Transcriptome Analysis	During locomotion trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change rather than the locomotor frequency. The brainstem steering neurons are in turn controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg gly2: GFP zebrafish brain stem one cell from each fish a total of eight fish				Glycinergic neurons m17	GSM8807155		tissue:Glycinergic neurons\|cell type:Glycinergic neurons\|genotype:Tg gly2: GFP\|geo loc name:missing\|collection date:missing	Glycinergic neurons m17	Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.	Glycinergic neurons	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.	cell type:Glycinergic neurons\|genotype:Tg gly2: GFP	GSM8807155	GSM8807155: Glycinergic neurons m17; Danio rerio; RNA Seq	GSM8807155 r1	GSM8807155	1	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP565442			M17_1.fq.gz M17_2.fq.gz	fastq fastq	7922316510.0	28870507.0	GSM8807155 r1		A:2259269798;C:1309791881;G:1358854827;T:2993890708;N:509296			2259269798	1309791881	1358854827	2993890708	509296	SRX27754020	SRS24139551	SRA2081247	TongJi university	TongJi university												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2025-02-21	Undetermined	Undetermined	Brain	Nervous System
34926	34926	SRR32424866	SRX27754019	SRS24139550	SRP565442	PRJNA1226487	Separate brainstem circuits for fast steering and slow exploratory turns	GSE290157	Transcriptome Analysis	During locomotion trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change rather than the locomotor frequency. The brainstem steering neurons are in turn controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg gly2: GFP zebrafish brain stem one cell from each fish a total of eight fish				Glycinergic neurons m16	GSM8807154		tissue:Glycinergic neurons\|cell type:Glycinergic neurons\|genotype:Tg gly2: GFP\|geo loc name:missing\|collection date:missing	Glycinergic neurons m16	Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.	Glycinergic neurons	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.	cell type:Glycinergic neurons\|genotype:Tg gly2: GFP	GSM8807154	GSM8807154: Glycinergic neurons m16; Danio rerio; RNA Seq	GSM8807154 r1	GSM8807154	1	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP565442			M16_1.fq.gz M16_2.fq.gz	fastq fastq	7720739055.0	27919217.0	GSM8807154 r1		A:2250075980;C:1271393485;G:1306175216;T:2892579232;N:515142			2250075980	1271393485	1306175216	2892579232	515142	SRX27754019	SRS24139550	SRA2081247	TongJi university	TongJi university												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2025-02-21	Undetermined	Undetermined	Brain	Nervous System
34927	34927	SRR32424867	SRX27754018	SRS24139549	SRP565442	PRJNA1226487	Separate brainstem circuits for fast steering and slow exploratory turns	GSE290157	Transcriptome Analysis	During locomotion trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change rather than the locomotor frequency. The brainstem steering neurons are in turn controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg gly2: GFP zebrafish brain stem one cell from each fish a total of eight fish				Glycinergic neurons m11	GSM8807153		tissue:Glycinergic neurons\|cell type:Glycinergic neurons\|genotype:Tg gly2: GFP\|geo loc name:missing\|collection date:missing	Glycinergic neurons m11	Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.	Glycinergic neurons	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.	cell type:Glycinergic neurons\|genotype:Tg gly2: GFP	GSM8807153	GSM8807153: Glycinergic neurons m11; Danio rerio; RNA Seq	GSM8807153 r1	GSM8807153	1	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP565442			M11_1.fq.gz M11_2.fq.gz	fastq fastq	6830992776.0	24127264.0	GSM8807153 r1		A:1949282464;C:1265666713;G:1276892181;T:2338677805;N:473613			1949282464	1265666713	1276892181	2338677805	473613	SRX27754018	SRS24139549	SRA2081247	TongJi university	TongJi university												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2025-02-21	Undetermined	Undetermined	Brain	Nervous System
34928	34928	SRR32424868	SRX27754017	SRS24139548	SRP565442	PRJNA1226487	Separate brainstem circuits for fast steering and slow exploratory turns	GSE290157	Transcriptome Analysis	During locomotion trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change rather than the locomotor frequency. The brainstem steering neurons are in turn controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg gly2: GFP zebrafish brain stem one cell from each fish a total of eight fish				Glycinergic neurons m9	GSM8807152		tissue:Glycinergic neurons\|cell type:Glycinergic neurons\|genotype:Tg gly2: GFP\|geo loc name:missing\|collection date:missing	Glycinergic neurons m9	Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.	Glycinergic neurons	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.	cell type:Glycinergic neurons\|genotype:Tg gly2: GFP	GSM8807152	GSM8807152: Glycinergic neurons m9; Danio rerio; RNA Seq	GSM8807152 r1	GSM8807152	1	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP565442			M9_1.fq.gz M9_2.fq.gz	fastq fastq	7582940148.0	27320994.0	GSM8807152 r1		A:2107584201;C:1339317674;G:1381218723;T:2754261953;N:557597			2107584201	1339317674	1381218723	2754261953	557597	SRX27754017	SRS24139548	SRA2081247	TongJi university	TongJi university												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2025-02-21	Undetermined	Undetermined	Brain	Nervous System
34929	34929	SRR32424869	SRX27754016	SRS24139547	SRP565442	PRJNA1226487	Separate brainstem circuits for fast steering and slow exploratory turns	GSE290157	Transcriptome Analysis	During locomotion trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change rather than the locomotor frequency. The brainstem steering neurons are in turn controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg gly2: GFP zebrafish brain stem one cell from each fish a total of eight fish				Glycinergic neurons m6	GSM8807151		tissue:Glycinergic neurons\|cell type:Glycinergic neurons\|genotype:Tg gly2: GFP\|geo loc name:missing\|collection date:missing	Glycinergic neurons m6	Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.	Glycinergic neurons	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.	cell type:Glycinergic neurons\|genotype:Tg gly2: GFP	GSM8807151	GSM8807151: Glycinergic neurons m6; Danio rerio; RNA Seq	GSM8807151 r1	GSM8807151	1	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP565442			M6_1.fq.gz M6_2.fq.gz	fastq fastq	7719009952.0	27333519.0	GSM8807151 r1		A:2131513261;C:1443134919;G:1469022783;T:2672576370;N:2762619			2131513261	1443134919	1469022783	2672576370	2762619	SRX27754016	SRS24139547	SRA2081247	TongJi university	TongJi university												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2025-02-21	Undetermined	Undetermined	Brain	Nervous System
34930	34930	SRR32424870	SRX27754015	SRS24139546	SRP565442	PRJNA1226487	Separate brainstem circuits for fast steering and slow exploratory turns	GSE290157	Transcriptome Analysis	During locomotion trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change rather than the locomotor frequency. The brainstem steering neurons are in turn controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg gly2: GFP zebrafish brain stem one cell from each fish a total of eight fish				Glycinergic neurons m5	GSM8807150		tissue:Glycinergic neurons\|cell type:Glycinergic neurons\|genotype:Tg gly2: GFP\|geo loc name:missing\|collection date:missing	Glycinergic neurons m5	Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.	Glycinergic neurons	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.	cell type:Glycinergic neurons\|genotype:Tg gly2: GFP	GSM8807150	GSM8807150: Glycinergic neurons m5; Danio rerio; RNA Seq	GSM8807150 r1	GSM8807150	1	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP565442			M5_1.fq.gz M5_2.fq.gz	fastq fastq	8381104622.0	30664708.0	GSM8807150 r1		A:2289409726;C:1427540731;G:1492945660;T:3168884923;N:2323582			2289409726	1427540731	1492945660	3168884923	2323582	SRX27754015	SRS24139546	SRA2081247	TongJi university	TongJi university												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2025-02-21	Undetermined	Undetermined	Brain	Nervous System
34931	34931	SRR32424871	SRX27754014	SRS24139545	SRP565442	PRJNA1226487	Separate brainstem circuits for fast steering and slow exploratory turns	GSE290157	Transcriptome Analysis	During locomotion trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change rather than the locomotor frequency. The brainstem steering neurons are in turn controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg gly2: GFP zebrafish brain stem one cell from each fish a total of eight fish				Glycinergic neurons m2	GSM8807149		tissue:Glycinergic neurons\|cell type:Glycinergic neurons\|genotype:Tg gly2: GFP\|geo loc name:missing\|collection date:missing	Glycinergic neurons m2	Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.	Glycinergic neurons	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.	cell type:Glycinergic neurons\|genotype:Tg gly2: GFP	GSM8807149	GSM8807149: Glycinergic neurons m2; Danio rerio; RNA Seq	GSM8807149 r1	GSM8807149	1	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP565442			M2_1.fq.gz M2_2.fq.gz	fastq fastq	8672887150.0	31410837.0	GSM8807149 r1		A:2358621884;C:1534269208;G:1583773576;T:3192613040;N:3609442			2358621884	1534269208	1583773576	3192613040	3609442	SRX27754014	SRS24139545	SRA2081247	TongJi university	TongJi university												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2025-02-21	Undetermined	Undetermined	Brain	Nervous System
34932	34932	SRR32424872	SRX27754013	SRS24139544	SRP565442	PRJNA1226487	Separate brainstem circuits for fast steering and slow exploratory turns	GSE290157	Transcriptome Analysis	During locomotion trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change rather than the locomotor frequency. The brainstem steering neurons are in turn controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg gly2: GFP zebrafish brain stem one cell from each fish a total of eight fish				Glycinergic neurons m1	GSM8807148		tissue:Glycinergic neurons\|cell type:Glycinergic neurons\|genotype:Tg gly2: GFP\|geo loc name:missing\|collection date:missing	Glycinergic neurons m1	Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.	Glycinergic neurons	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.	cell type:Glycinergic neurons\|genotype:Tg gly2: GFP	GSM8807148	GSM8807148: Glycinergic neurons m1; Danio rerio; RNA Seq	GSM8807148 r1	GSM8807148	1	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP565442			M1_1.fq.gz M1_2.fq.gz	fastq fastq	30591542380.0	110161442.0	GSM8807148 r1		A:8730028799;C:5294263499;G:5420191319;T:11143275950;N:3782813			8730028799	5294263499	5420191319	11143275950	3782813	SRX27754013	SRS24139544	SRA2081247	TongJi university	TongJi university												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2025-02-21	Undetermined	Undetermined	Brain	Nervous System
40482	40482	SRR3183446	SRX1597282	SRS1307292	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		mac repair2	GSM2069441		source name:mac repair\|strain:ABGO\|fluorescence:Kaedared\|lesion stg:macrophage traction\|tissue:brain\|cell type:Macrophage	mac repair2	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	mac repair	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Kaedared\|lesion stg:macrophage traction\|tissue:brain\|cell type:Macrophage	GSM2069441	GSM2069441: mac repair2; Danio rerio; RNA Seq	GSM2069441		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069441	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			mac-repair4-SC038_1.fq.gz mac-repair4-SC038_2.fq.gz	fastq fastq	5301635532.0	26540791.0	GSM2069441 r1	0:99.88 1:99.88	A:1455876159;C:1213611469;G:1209697136;T:1422373935;N:76833	99	99	1455876159	1213611469	1209697136	1422373935	76833	SRX1597282	SRS1307292	SRA356990	GEO	SouthWest university Of China	2	0.90904	0.90891	0.13484	0.13454	0.75566	0.75517	0.54043	0.5377	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40483	40483	SRR3183445	SRX1597281	SRS1307293	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		mac con2	GSM2069440		source name:mac con\|strain:ABGO\|fluorescence:Kaedared\|lesion stg:uninjured control\|tissue:brain\|cell type:Macrophage	mac con2	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	mac con	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Kaedared\|lesion stg:uninjured control\|tissue:brain\|cell type:Macrophage	GSM2069440	GSM2069440: mac con2; Danio rerio; RNA Seq	GSM2069440		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069440	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			mac-con2-SC019_2.fq.gz mac-con2-SC019_1.fq.gz	fastq fastq	6320110276.0	31638738.0	GSM2069440 r1	0:99.88 1:99.88	A:1939242414;C:1232507136;G:1227176155;T:1921089930;N:94641	99	99	1939242414	1232507136	1227176155	1921089930	94641	SRX1597281	SRS1307293	SRA356990	GEO	SouthWest university Of China	2	0.83136	0.8313	0.58017	0.58041	0.86628	0.86669	0.59968	0.59677	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40484	40484	SRR3183444	SRX1597280	SRS1307294	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		mac ab2	GSM2069439		source name:mac ab\|strain:ABGO\|fluorescence:Kaedared\|lesion stg:macrophage arrival\|tissue:brain\|cell type:Macrophage	mac ab2	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	mac ab	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Kaedared\|lesion stg:macrophage arrival\|tissue:brain\|cell type:Macrophage	GSM2069439	GSM2069439: mac ab2; Danio rerio; RNA Seq	GSM2069439		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069439	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			mac-ab3-SC035_1.fq.gz mac-ab3-SC035_2.fq.gz	fastq fastq	6565165025.0	32864923.0	GSM2069439 r1										SRX1597280	SRS1307294	SRA356990	GEO	SouthWest university Of China	2	0.93107	0.92872	0.26305	0.26195	0.82686	0.82712	0.54026	0.54	100	98	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40485	40485	SRR3183443	SRX1597279	SRS1307295	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		EC repair2	GSM2069438		source name:EC repair\|strain:ABGO\|fluorescence:Dendra2red\|lesion stg:macrophage traction\|tissue:brain\|cell type:Endothelial cell	EC repair2	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	EC repair	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Dendra2red\|lesion stg:macrophage traction\|tissue:brain\|cell type:Endothelial cell	GSM2069438	GSM2069438: EC repair2; Danio rerio; RNA Seq	GSM2069438		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069438	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			EC-repair2-SC028_1.fq.gz EC-repair2-SC028_2.fq.gz	fastq fastq	5464573374.0	27356971.0	GSM2069438 r1	0:99.88 1:99.88	A:1574953192;C:1193040049;G:1183625694;T:1512874939;N:79500	99	99	1574953192	1193040049	1183625694	1512874939	79500	SRX1597279	SRS1307295	SRA356990	GEO	SouthWest university Of China	2	0.89166	0.8896	0.27558	0.27603	0.87278	0.87221	0.60926	0.60627	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40486	40486	SRR3183442	SRX1597278	SRS1307296	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		EC con2	GSM2069437		source name:EC con\|strain:ABGO\|fluorescence:Dendra2red\|lesion stg:uninjured control\|tissue:brain\|cell type:Endothelial cell	EC con2	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	EC con	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Dendra2red\|lesion stg:uninjured control\|tissue:brain\|cell type:Endothelial cell	GSM2069437	GSM2069437: EC con2; Danio rerio; RNA Seq	GSM2069437		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069437	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			EC-con2-SC022_2.fq.gz EC-con2-SC022_1.fq.gz	fastq fastq	5812259006.0	29094912.0	GSM2069437 r1	0:99.88 1:99.88	A:1668770504;C:1266987641;G:1260647092;T:1615770218;N:83551	99	99	1668770504	1266987641	1260647092	1615770218	83551	SRX1597278	SRS1307296	SRA356990	GEO	SouthWest university Of China	2	0.8919	0.89162	0.25452	0.25485	0.83347	0.83392	0.559	0.55795	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40487	40487	SRR3183441	SRX1597277	SRS1307297	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		EC ab1	GSM2069436		source name:EC ab\|strain:ABGO\|fluorescence:Dendra2red\|lesion stg:macrophage arrival\|tissue:brain\|cell type:Endothelial cell	EC ab1	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	EC ab	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Dendra2red\|lesion stg:macrophage arrival\|tissue:brain\|cell type:Endothelial cell	GSM2069436	GSM2069436: EC ab1; Danio rerio; RNA Seq	GSM2069436		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069436	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			Ec-ab3-SC030_2.fq.gz Ec-ab3-SC030_1.fq.gz	fastq fastq	4865614309.0	24358874.0	GSM2069436 r1	0:99.87 1:99.87	A:1413472486;C:1059060950;G:1037673850;T:1355336145;N:70878	99	99	1413472486	1059060950	1037673850	1355336145	70878	SRX1597277	SRS1307297	SRA356990	GEO	SouthWest university Of China	2	0.87852	0.8772	0.28182	0.28242	0.89057	0.89096	0.73919	0.73928	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40488	40488	SRR3183440	SRX1597276	SRS1307298	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		Ec ab2	GSM2069435		source name:EC ab\|strain:ABGO\|fluorescence:Dendra2red\|lesion stg:macrophage arrival\|tissue:brain\|cell type:Endothelial cell	Ec ab2	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	EC ab	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Dendra2red\|lesion stg:macrophage arrival\|tissue:brain\|cell type:Endothelial cell	GSM2069435	GSM2069435: Ec ab2; Danio rerio; RNA Seq	GSM2069435		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069435	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			Ec-ab2-SC026_2.fq.gz Ec-ab2-SC026_1.fq.gz	fastq fastq	6707716689.0	33577941.0	GSM2069435 r1	0:99.88 1:99.88	A:1928489398;C:1460549435;G:1448129164;T:1870450597;N:98095	99	99	1928489398	1460549435	1448129164	1870450597	98095	SRX1597276	SRS1307298	SRA356990	GEO	SouthWest university Of China	2	0.92184	0.9211	0.21351	0.21381	0.78242	0.78246	0.54924	0.54828	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40489	40489	SRR3183439	SRX1597275	SRS1307299	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		mac repair1	GSM2069434		source name:mac repair\|strain:ABGO\|fluorescence:Kaedared\|lesion stg:macrophage traction\|tissue:brain\|cell type:Macrophage	mac repair1	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	mac repair	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Kaedared\|lesion stg:macrophage traction\|tissue:brain\|cell type:Macrophage	GSM2069434	GSM2069434: mac repair1; Danio rerio; RNA Seq	GSM2069434		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069434	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			mac-repair-3-11_1.fq.gz mac-repair-3-11_2.fq.gz	fastq fastq	4119165097.0	20619633.0	GSM2069434 r1	0:99.88 1:99.88	A:1220355632;C:853066472;G:852272936;T:1193322733;N:147324	99	99	1220355632	853066472	852272936	1193322733	147324	SRX1597275	SRS1307299	SRA356990	GEO	SouthWest university Of China	2	0.91892	0.91808	0.30064	0.30083	0.8379	0.83812	0.56301	0.5643	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40490	40490	SRR3183438	SRX1597274	SRS1307300	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		mac con1	GSM2069433		source name:mac con\|strain:ABGO\|fluorescence:Kaedared\|lesion stg:uninjured control\|tissue:brain\|cell type:Macrophage	mac con1	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	mac con	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Kaedared\|lesion stg:uninjured control\|tissue:brain\|cell type:Macrophage	GSM2069433	GSM2069433: mac con1; Danio rerio; RNA Seq	GSM2069433		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069433	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			mac-con-2-26_2.fq.gz mac-con-2-26_1.fq.gz	fastq fastq	5593489486.0	27999140.0	GSM2069433 r1	0:99.89 1:99.89	A:1625139429;C:1195509047;G:1187687983;T:1585113551;N:39476	99	99	1625139429	1195509047	1187687983	1585113551	39476	SRX1597274	SRS1307300	SRA356990	GEO	SouthWest university Of China	2	0.91078	0.91073	0.29885	0.30068	0.83167	0.83244	0.62474	0.6305	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40491	40491	SRR3183437	SRX1597273	SRS1307301	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		mac ab1	GSM2069432		source name:mac ab\|strain:ABGO\|fluorescence:Kaedared\|lesion stg:macrophage arrival\|tissue:brain\|cell type:Macrophage	mac ab1	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	mac ab	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Kaedared\|lesion stg:macrophage arrival\|tissue:brain\|cell type:Macrophage	GSM2069432	GSM2069432: mac ab1; Danio rerio; RNA Seq	GSM2069432		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069432	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			mac-ab-3-4_1.fq.gz mac-ab-3-4_2.fq.gz	fastq fastq	5218899449.0	26123043.0	GSM2069432 r1	0:99.89 1:99.89	A:1547095822;C:1077774232;G:1071111992;T:1522880692;N:36711	99	99	1547095822	1077774232	1071111992	1522880692	36711	SRX1597273	SRS1307301	SRA356990	GEO	SouthWest university Of China	2	0.80093	0.80114	0.34662	0.34753	0.84431	0.84528	0.45488	0.58269	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40492	40492	SRR3183436	SRX1597272	SRS1307302	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		EC repair1	GSM2069431		source name:EC repair\|strain:ABGO\|fluorescence:Dendra2red\|lesion stg:macrophage traction\|tissue:brain\|cell type:Endothelial cell	EC repair1	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	EC repair	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Dendra2red\|lesion stg:macrophage traction\|tissue:brain\|cell type:Endothelial cell	GSM2069431	GSM2069431: EC repair1; Danio rerio; RNA Seq	GSM2069431		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069431	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			EC-repair-3-12_1.fq.gz EC-repair-3-12_2.fq.gz	fastq fastq	4074593965.0	20396835.0	GSM2069431 r1	0:99.88 1:99.88	A:1183916478;C:879516439;G:873592591;T:1137385419;N:183038	99	99	1183916478	879516439	873592591	1137385419	183038	SRX1597272	SRS1307302	SRA356990	GEO	SouthWest university Of China	2	0.91437	0.91374	0.17815	0.179	0.8504	0.85141	0.56489	0.56038	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	Brain	Nervous System
40493	40493	SRR3183435	SRX1597271	SRS1307303	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		EC con1	GSM2069430		source name:EC con\|strain:ABGO\|fluorescence:Dendra2red\|lesion stg:uninjured control\|tissue:brain\|cell type:Endothelial cell	EC con1	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	EC con	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	strain:ABGO\|fluorescence:Dendra2red\|lesion stg:uninjured control\|tissue:brain\|cell type:Endothelial cell	GSM2069430	GSM2069430: EC con1; Danio rerio; RNA Seq	GSM2069430		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069430	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP070686			EC-con-2-27_2.fq.gz	fastq	5255670920.0	26309124.0	GSM2069430 r1	0:99.88 1:99.88	A:1577945764;C:1073541139;G:1067712819;T:1536399615;N:71583	99	99	1577945764	1073541139	1067712819	1536399615	71583	SRX1597271	SRS1307303	SRA356990	GEO	SouthWest university Of China	2	0.87619	0.87775	0.42791	0.42947	0.88509	0.88645	0.63901	0.63893	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2016-02-23	Larval	Larval	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");;