metadata: run_metadata: 403 rows where experiment.library_strategy = "RNA-Seq", technology = "generic-scrnaseq-only" and tissue

403 rows where experiment.library_strategy = "RNA-Seq", technology = "generic-scrnaseq-only" 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.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.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
26536	26536	SRR26130973	SRX21844394	SRS18942411	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.				10X49 2	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 6\|BioSampleModel:Model organism or animal							SC ZF Hypo6	10X49 2	10X49 2	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307		10X49_2_S5_L001_R1_001.fastq.gz 10X49_2_S5_L001_R2_001.fastq.gz 10X49_2_S5_L002_R1_001.fastq.gz 10X49_2_S5_L002_R2_001.fastq.gz 10X49_2_S5_L003_R1_001.fastq.gz 10X49_2_S5_L003_R2_001.fastq.gz 10X49_2_S5_L004_R1_001.fastq.gz 10X49_2_S5_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	3126113844.0	37215641.0	10X49 2 S5 L001 R1 001.fastq.gz	0:28 1:56	A:898881980;C:657306128;G:664563758;T:905262774;N:99204	28	56	898881980	657306128	664563758	905262774	99204	SRX21844394	SRS18942411	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.01241	0.88203	0.00542	0.35268	0.98129	0.7586	0.40274	0.5074	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26537	26537	SRR26130974	SRX21844393	SRS18942407	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.				10X49 1	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 5\|BioSampleModel:Model organism or animal							SC ZF Hypo5	10X49 1	10X49 1	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307		10X49_1_S4_L001_R1_001.fastq.gz 10X49_1_S4_L001_R2_001.fastq.gz 10X49_1_S4_L002_R1_001.fastq.gz 10X49_1_S4_L002_R2_001.fastq.gz 10X49_1_S4_L003_R1_001.fastq.gz 10X49_1_S4_L003_R2_001.fastq.gz 10X49_1_S4_L004_R1_001.fastq.gz 10X49_1_S4_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	3315364752.0	39468628.0	10X49 1 S4 L001 R1 001.fastq.gz	0:28 1:56	A:957164498;C:690985782;G:704099796;T:963009918;N:104758	28	56	957164498	690985782	704099796	963009918	104758	SRX21844393	SRS18942407	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.0143	0.88325	0.00601	0.35854	0.97816	0.75868	0.4158	0.50825	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26538	26538	SRR26130975	SRX21844392	SRS18942399	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.				10X47 2	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 4\|BioSampleModel:Model organism or animal							SC ZF Hypo4	10X47 2	10X47 2	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307		10X47_2_S2_L001_R1_001.fastq.gz 10X47_2_S2_L001_R2_001.fastq.gz 10X47_2_S2_L002_R1_001.fastq.gz 10X47_2_S2_L002_R2_001.fastq.gz 10X47_2_S2_L003_R1_001.fastq.gz 10X47_2_S2_L003_R2_001.fastq.gz 10X47_2_S2_L004_R1_001.fastq.gz 10X47_2_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	3525979800.0	41975950.0	10X47 2 S2 L001 R1 001.fastq.gz	0:28 1:56	A:1030048762;C:725438274;G:855378888;T:915005070;N:108806	28	56	1030048762	725438274	855378888	915005070	108806	SRX21844392	SRS18942399	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.0126	0.69252	0.00546	0.25721	0.98005	0.85295	0.39068	0.51992	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26539	26539	SRR26130976	SRX21844391	SRS18942406	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.				10X47 1	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 3\|BioSampleModel:Model organism or animal							SC ZF Hypo3	10X47 1	10X47 1	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307		10X47_1_S1_L001_R1_001.fastq.gz 10X47_1_S1_L001_R2_001.fastq.gz 10X47_1_S1_L002_R1_001.fastq.gz 10X47_1_S1_L002_R2_001.fastq.gz 10X47_1_S1_L003_R1_001.fastq.gz 10X47_1_S1_L003_R2_001.fastq.gz 10X47_1_S1_L004_R1_001.fastq.gz 10X47_1_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	3288490212.0	39148693.0	10X47 1 S1 L001 R1 001.fastq.gz	0:28 1:56	A:950740376;C:692224998;G:723085676;T:922337432;N:101730	28	56	950740376	692224998	723085676	922337432	101730	SRX21844391	SRS18942406	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.01086	0.86383	0.0052	0.31674	0.98244	0.78309	0.39399	0.52299	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26540	26540	SRR26130977	SRX21844390	SRS18942410	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.				10X39 2	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 2\|BioSampleModel:Model organism or animal							SC ZF Hypo2	10X39 2	10X39 2	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307		10X39_2_S2_L001_R1_001.fastq.gz 10X39_2_S2_L001_R2_001.fastq.gz 10X39_2_S2_L002_R1_001.fastq.gz 10X39_2_S2_L002_R2_001.fastq.gz 10X39_2_S2_L003_R1_001.fastq.gz 10X39_2_S2_L003_R2_001.fastq.gz 10X39_2_S2_L004_R1_001.fastq.gz 10X39_2_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	20594785932.0	245176023.0	10X39 2 S2 L001 R1 001.fastq.gz	0:28 1:56	A:5909286071;C:4378110318;G:4489721587;T:5804002561;N:13665395	28	56	5909286071	4378110318	4489721587	5804002561	13665395	SRX21844390	SRS18942410	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.01117	0.90005	0.00416	0.25843	0.98056	0.77926	0.45338	0.53366	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26541	26541	SRR26130978	SRX21844389	SRS18942405	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.				10X39 1	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 1\|BioSampleModel:Model organism or animal							SC ZF Hypo1	10X39 1	10X39 1	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307		10X39_1_S1_L004_R2_001.fastq.gz 10X39_1_S1_L004_R1_001.fastq.gz 10X39_1_S1_L003_R2_001.fastq.gz 10X39_1_S1_L003_R1_001.fastq.gz 10X39_1_S1_L002_R2_001.fastq.gz 10X39_1_S1_L002_R1_001.fastq.gz 10X39_1_S1_L001_R2_001.fastq.gz 10X39_1_S1_L001_R1_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	13293718116.0	158258549.0	10X39 1 S1 L001 R1 001.fastq.gz	0:28 1:56	A:3791388201;C:2833705086;G:2863082386;T:3796683434;N:8859009	28	56	3791388201	2833705086	2863082386	3796683434	8859009	SRX21844389	SRS18942405	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.01078	0.90504	0.00392	0.24179	0.98098	0.77741	0.42922	0.52858	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
30691	30691	SRR28270998	SRX23880961	SRS20704477	SRP494117	PRJNA1085662	Roxithromycin exposure induces motoneuron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells	PRJNA1085662	Other	Roxithromycin ROX a commonly used macrolide antibiotic is extensively employed in human medicine and livestock industries. Due to its structural stability and resistance to biological degradation ROX persists as a resilient environmental contaminant detectable in aquatic ecosystems and food products. However our understanding of the potential health risks to humans from continuous ROX exposure remains limited. In this study we used the zebrafish as a vertebrate model to explore the potential developmental toxicity of early ROX exposure particularly focusing on its effects on locomotor functionality and motoneuron development. Early exposure to ROX induces marked developmental toxicity in zebrafish embryos significantly reducing hatch rates body lengths and increased malformation rates. Moreover ROX exposure adversely affected the locomotive capacity of zebrafish embryos and observations in transgenic zebrafish Tghb9:eGFP revealed axonal loss in motor neurons evident through reduced or irregular axonal lengths. Concurrently abnormal apoptosis in ROX exposed zebrafish embryos intensified alongside the upregulation of apoptosis related genes bax bcl2 caspase 3a. Single cell sequencing further disclosed substantial effects of ROX on genes involved in the differentiation of motor neuron progenitor cells ngn1 olig2 axon development cd82a mbpa plp1b sema5a and neuroimmunity aplnrb aplnra in zebrafish larvae. Furthermore the motor neuron defects induced by ROX can be rescued by administering ngn1 agonist. In summary ROX exposure leads to early life abnormalities in zebrafish motor neurons and locomotor behavior by hindering the differentiation of motor neuron progenitor cells and inducing abnormal apoptosis.				WT	strain:not provided\|isolate:not provided\|breed:not provided\|cultivar:not provided\|ecotype:not provided\|age:not provided\|dev stage:not provided\|collection date:not provided\|geo loc name:not provided\|sex:not provided\|tissue:Cerebrum\|BioSampleModel:Model organism or animal							Roxithromycin exposure induces mot1uron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells	DANIO	DANIO	Illumina Second Generation Sequencing			RNA-Seq	TRANSCRIPTOMIC	cDNA_oligo_dT	SINGLE	BGISEQ	BGISEQ-500	SRP494117		WT_S1_L001_I1_001.fastq.gz	fastq	7991376264.0	998922033.0	WT S1 L001 I1 001.fastq.gz	0:8	A:2573734851;C:1426474966;G:1492966198;T:2498173074;N:27175	8		2573734851	1426474966	1492966198	2498173074	27175	SRX23880961	SRS20704477	SRA1820072	shantou university\|Neurobiology Center	shantou university	1	0.0		0.0		1.0				8		T		under 1.2% mapping rate	bgi	bgi	unknown	poly_a	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-03-11	Undetermined	Multi-stage	Brain	Nervous System
34262	34262	SRR31595085	SRX26959911	SRS23429841	SRP549196	PRJNA1193812	Single cell transcriptome sequencing of zebrafish olfactory epithelium	PRJNA1193812	Other	We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.		Alarm substances treatment Group		CAS	strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:1 year old\|dev stage:adult CAS group\|collection date:2020 10 10\|geo loc name:China: Wuhan\|sex:male\|tissue:Olfactory epithelium CAS group\|BioSampleModel:Model organism or animal							Single cell transcriptome of the AB zebrafish olfactory epithelium post treatment with alarm substances	CAS OE	CAS OE	sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	NextSeq 550	SRP549196		CAS_S1_L001_R1_001.fastq.gz CAS_S1_L001_R2_001.fastq.gz	fastq fastq	54518124857.0	458135503.0	CAS S1 L001 R1 001.fastq.gz	0:28 1:91	A:15384916510;C:12274547586;G:14008767028;T:12837270924;N:12622809	28	91	15384916510	12274547586	14008767028	12837270924	12622809	SRX26959911	SRS23429841	SRA2027027	Institute of Hydrobiology, Chinese Academy of Sciences\|Chinese Academy of Sciences	Institute of Hydrobiology, Chinese Academy of Sciences												T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2024-12-04	Adult	Adult	Brain	Nervous System
34263	34263	SRR31595086	SRX26959910	SRS23429840	SRP549196	PRJNA1193812	Single cell transcriptome sequencing of zebrafish olfactory epithelium	PRJNA1193812	Other	We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.		Blank control group		CTR	strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:1 year old\|dev stage:adult CTR group\|collection date:2020 10 10\|geo loc name:China: Wuhan\|sex:male\|tissue:Olfactory epithelium CTR group\|BioSampleModel:Model organism or animal							Single cell transcriptome of the AB strain zebrafish olfactory epithelium	CTR OE	CTR OE	sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	NextSeq 550	SRP549196		CTR_S1_L001_R1_001.fastq.gz CTR_S1_L001_R2_001.fastq.gz	fastq fastq	50773421790.0	426667410.0	CTR S1 L001 R1 001.fastq.gz	0:28 1:91	A:14105926130;C:11510784907;G:13135577448;T:12011516484;N:9616821	28	91	14105926130	11510784907	13135577448	12011516484	9616821	SRX26959910	SRS23429840	SRA2027027	Institute of Hydrobiology, Chinese Academy of Sciences\|Chinese Academy of Sciences	Institute of Hydrobiology, Chinese Academy of Sciences												T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2024-12-04	Adult	Adult	Brain	Nervous System
54345	54345	SRR10126111	SRX6854760	SRS5392962	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 1 01 E02	GSM4080997	tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.0813302707773932	RG 1 01 E02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.0813302707773932	GSM4080997	GSM4080997: RG 1 01 E02; Danio rerio; RNA Seq	GSM4080997		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080997	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23839_RG_1_01_E02.bam	bam	16444652.0	216377.0	GSM4080997 r1	0:76	A:4583352;C:3984328;G:3906383;T:3970500;N:89	76		4583352	3984328	3906383	3970500	89	SRX6854760	SRS5392962	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.26908		0.09242		0.99825		0.67661		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54346	54346	SRR10126110	SRX6854759	SRS5392961	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 1 01 B02	GSM4080996	tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.137111856361026	RG 1 01 B02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.137111856361026	GSM4080996	GSM4080996: RG 1 01 B02; Danio rerio; RNA Seq	GSM4080996		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080996	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23836_RG_1_01_B02.bam	bam	14345076.0	188751.0	GSM4080996 r1	0:76	A:4237579;C:3235570;G:3240300;T:3631525;N:102	76		4237579	3235570	3240300	3631525	102	SRX6854759	SRS5392961	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.37026		0.12862		0.99805		0.83484		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54347	54347	SRR10126109	SRX6854758	SRS5392960	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 1 01 C01	GSM4080995	tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.596981146320204	RG 1 01 C01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.596981146320204	GSM4080995	GSM4080995: RG 1 01 C01; Danio rerio; RNA Seq	GSM4080995		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080995	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23829_RG_1_01_C01_mod.bam	bam	44287252.0	582727.0	GSM4080995 r1	0:76	A:12057290;C:10158222;G:10161190;T:11910345;N:205	76		12057290	10158222	10161190	11910345	205	SRX6854758	SRS5392960	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.83606		0.11078		0.97364		0.51554		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54348	54348	SRR10126108	SRX6854757	SRS5392959	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 1 01 G02	GSM4080994	tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.336437957921624	RG 1 01 G02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.336437957921624	GSM4080994	GSM4080994: RG 1 01 G02; Danio rerio; RNA Seq	GSM4080994		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080994	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23841_RG_1_01_G02_mod.bam	bam	18090356.0	238031.0	GSM4080994 r1	0:76	A:5124071;C:4154073;G:4123933;T:4688206;N:73	76		5124071	4154073	4123933	4688206	73	SRX6854757	SRS5392959	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.63512		0.05239		0.99257		0.67835		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54349	54349	SRR10126107	SRX6854756	SRS5392958	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 1 01 F02	GSM4080993	tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.169583947726024	RG 1 01 F02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.169583947726024	GSM4080993	GSM4080993: RG 1 01 F02; Danio rerio; RNA Seq	GSM4080993		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080993	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23840_RG_1_01_F02.bam	bam	13143060.0	172935.0	GSM4080993 r1	0:76	A:3676240;C:3051166;G:3081467;T:3334128;N:59	76		3676240	3051166	3081467	3334128	59	SRX6854756	SRS5392958	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.4252		0.0971		0.99697		0.81536		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54350	54350	SRR10126106	SRX6854755	SRS5392957	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON30 01 F12	GSM4080992	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.307951918399687	ON30 01 F12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.307951918399687	GSM4080992	GSM4080992: ON30 01 F12; Danio rerio; RNA Seq	GSM4080992		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080992	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22296_ON30_01_F12_mod.bam	bam	45464644.0	598219.0	GSM4080992 r1	0:76	A:13070969;C:9463048;G:9617299;T:13313099;N:229	76		13070969	9463048	9617299	13313099	229	SRX6854755	SRS5392957	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.85125		0.28428		0.94795		0.49176		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54351	54351	SRR10126105	SRX6854754	SRS5392956	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG31 01 H12	GSM4080991	tissue:Brain\|sorting:RG\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.349622553699452	RG31 01 H12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.349622553699452	GSM4080991	GSM4080991: RG31 01 H12; Danio rerio; RNA Seq	GSM4080991		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080991	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22298_RG31_01_H12_mod.bam	bam	54043448.0	711098.0	GSM4080991 r1	0:76	A:14990424;C:11836357;G:12008841;T:15207589;N:237	76		14990424	11836357	12008841	15207589	237	SRX6854754	SRS5392956	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.85818		0.139		0.95706		0.49646		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54352	54352	SRR10126104	SRX6854753	SRS5392955	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON29 01 E12	GSM4080990	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.270605518893939	ON29 01 E12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.270605518893939	GSM4080990	GSM4080990: ON29 01 E12; Danio rerio; RNA Seq	GSM4080990		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080990	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22295_ON29_01_E12_mod.bam	bam	31968716.0	420641.0	GSM4080990 r1	0:76	A:9066610;C:6733147;G:6934070;T:9234786;N:103	76		9066610	6733147	6934070	9234786	103	SRX6854753	SRS5392955	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.76341		0.34992		0.97583		0.47889		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54353	54353	SRR10126103	SRX6854752	SRS5392954	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON27 01 C12	GSM4080989	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.207435774030802	ON27 01 C12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.207435774030802	GSM4080989	GSM4080989: ON27 01 C12; Danio rerio; RNA Seq	GSM4080989		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080989	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22293_ON27_01_C12_mod.bam	bam	36635572.0	482047.0	GSM4080989 r1	0:76	A:10775220;C:6902317;G:7294618;T:11663244;N:173	76		10775220	6902317	7294618	11663244	173	SRX6854752	SRS5392954	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.6712		0.38208		0.98563		0.6672		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54354	54354	SRR10126102	SRX6854751	SRS5392953	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON28 01 D12	GSM4080988	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.361448206817182	ON28 01 D12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.361448206817182	GSM4080988	GSM4080988: ON28 01 D12; Danio rerio; RNA Seq	GSM4080988		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080988	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22294_ON28_01_D12_mod.bam	bam	48734088.0	641238.0	GSM4080988 r1	0:76	A:13468719;C:10758080;G:10910748;T:13596298;N:243	76		13468719	10758080	10910748	13596298	243	SRX6854751	SRS5392953	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.88752		0.18774		0.94911		0.46357		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54355	54355	SRR10126101	SRX6854750	SRS5392952	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON26 01 B12	GSM4080987	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.400282577622292	ON26 01 B12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.400282577622292	GSM4080987	GSM4080987: ON26 01 B12; Danio rerio; RNA Seq	GSM4080987		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080987	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22292_ON26_01_B12_mod.bam	bam	46093468.0	606493.0	GSM4080987 r1	0:76	A:12497312;C:10446137;G:10539301;T:12610508;N:210	76		12497312	10446137	10539301	12610508	210	SRX6854750	SRS5392952	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.89062		0.07593		0.95146		0.50127		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54356	54356	SRR10126100	SRX6854749	SRS5392951	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON25 01 A12	GSM4080986	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.36034551688211	ON25 01 A12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.36034551688211	GSM4080986	GSM4080986: ON25 01 A12; Danio rerio; RNA Seq	GSM4080986		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080986	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22291_ON25_01_A12_mod.bam	bam	56456068.0	742843.0	GSM4080986 r1	0:76	A:16017845;C:12025190;G:12186747;T:16226025;N:261	76		16017845	12025190	12186747	16226025	261	SRX6854749	SRS5392951	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87174		0.20317		0.94446		0.48709		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54357	54357	SRR10126099	SRX6854748	SRS5392950	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON24 01 H11	GSM4080985	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.324713155088674	ON24 01 H11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.324713155088674	GSM4080985	GSM4080985: ON24 01 H11; Danio rerio; RNA Seq	GSM4080985		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080985	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22290_ON24_01_H11_mod.bam	bam	49961108.0	657383.0	GSM4080985 r1	0:76	A:14127615;C:10704711;G:10835971;T:14292589;N:222	76		14127615	10704711	10835971	14292589	222	SRX6854748	SRS5392950	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87519		0.24291		0.91543		0.48833		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54358	54358	SRR10126098	SRX6854747	SRS5392949	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON20 01 D11	GSM4080984	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.345805160446015	ON20 01 D11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.345805160446015	GSM4080984	GSM4080984: ON20 01 D11; Danio rerio; RNA Seq	GSM4080984		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080984	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22286_ON20_01_D11_mod.bam	bam	45645220.0	600595.0	GSM4080984 r1	0:76	A:12652866;C:10016610;G:10144796;T:12830749;N:199	76		12652866	10016610	10144796	12830749	199	SRX6854747	SRS5392949	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.8612		0.21429		0.94649		0.51433		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54359	54359	SRR10126097	SRX6854746	SRS5392948	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON19 01 C11	GSM4080983	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.342848231466316	ON19 01 C11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.342848231466316	GSM4080983	GSM4080983: ON19 01 C11; Danio rerio; RNA Seq	GSM4080983		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080983	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22285_ON19_01_C11_mod.bam	bam	44588516.0	586691.0	GSM4080983 r1	0:76	A:12252079;C:9823426;G:9954660;T:12558164;N:187	76		12252079	9823426	9954660	12558164	187	SRX6854746	SRS5392948	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.8663		0.1874		0.95057		0.48221		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54360	54360	SRR10126096	SRX6854745	SRS5392947	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON18 01 B11	GSM4080982	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.356681923777462	ON18 01 B11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.356681923777462	GSM4080982	GSM4080982: ON18 01 B11; Danio rerio; RNA Seq	GSM4080982		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080982	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22284_ON18_01_B11_mod.bam	bam	41805776.0	550076.0	GSM4080982 r1	0:76	A:11557097;C:9225654;G:9383396;T:11639451;N:178	76		11557097	9225654	9383396	11639451	178	SRX6854745	SRS5392947	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.88353		0.19606		0.93237		0.49124		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54361	54361	SRR10126095	SRX6854744	SRS5392946	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON23 01 G11	GSM4080981	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.337622302046746	ON23 01 G11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.337622302046746	GSM4080981	GSM4080981: ON23 01 G11; Danio rerio; RNA Seq	GSM4080981		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080981	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22289_ON23_01_G11_mod.bam	bam	34314608.0	451508.0	GSM4080981 r1	0:76	A:9639586;C:7428852;G:7549525;T:9696492;N:153	76		9639586	7428852	7549525	9696492	153	SRX6854744	SRS5392946	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87321		0.25858		0.95168		0.504		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54362	54362	SRR10126094	SRX6854743	SRS5392945	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON22 01 F11	GSM4080980	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.351704193217474	ON22 01 F11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.351704193217474	GSM4080980	GSM4080980: ON22 01 F11; Danio rerio; RNA Seq	GSM4080980		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080980	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22288_ON22_01_F11_mod.bam	bam	47930388.0	630663.0	GSM4080980 r1	0:76	A:13368035;C:10449666;G:10572110;T:13540361;N:216	76		13368035	10449666	10572110	13540361	216	SRX6854743	SRS5392945	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87895		0.21319		0.92736		0.49859		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54363	54363	SRR10126093	SRX6854742	SRS5392944	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON21 01 E11	GSM4080979	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.330638956789342	ON21 01 E11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.330638956789342	GSM4080979	GSM4080979: ON21 01 E11; Danio rerio; RNA Seq	GSM4080979		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080979	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22287_ON21_01_E11_mod.bam	bam	46820788.0	616063.0	GSM4080979 r1	0:76	A:13360602;C:9787624;G:10022727;T:13649641;N:194	76		13360602	9787624	10022727	13649641	194	SRX6854742	SRS5392944	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.85652		0.23734		0.95629		0.49147		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54364	54364	SRR10126092	SRX6854741	SRS5392943	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON17 01 A11	GSM4080978	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.346374017705124	ON17 01 A11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.346374017705124	GSM4080978	GSM4080978: ON17 01 A11; Danio rerio; RNA Seq	GSM4080978		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080978	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22283_ON17_01_A11_mod.bam	bam	43871912.0	577262.0	GSM4080978 r1	0:76	A:12596782;C:9147890;G:9360119;T:12766904;N:217	76		12596782	9147890	9360119	12766904	217	SRX6854741	SRS5392943	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.86532		0.23115		0.95369		0.48216		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54365	54365	SRR10126091	SRX6854740	SRS5392942	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON11 01 C10	GSM4080977	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.352909893939849	ON11 01 C10	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.352909893939849	GSM4080977	GSM4080977: ON11 01 C10; Danio rerio; RNA Seq	GSM4080977		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080977	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22277_ON11_01_C10_mod.bam	bam	50586132.0	665607.0	GSM4080977 r1	0:76	A:14660026;C:10294910;G:10546028;T:15084936;N:232	76		14660026	10294910	10546028	15084936	232	SRX6854740	SRS5392942	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.85185		0.2673		0.95134		0.49125		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54366	54366	SRR10126090	SRX6854739	SRS5392941	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON15 01 G10	GSM4080976	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.253181242078581	ON15 01 G10	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.253181242078581	GSM4080976	GSM4080976: ON15 01 G10; Danio rerio; RNA Seq	GSM4080976		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080976	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22281_ON15_01_G10_mod.bam	bam	34478312.0	453662.0	GSM4080976 r1	0:76	A:10233215;C:6828213;G:6979097;T:10437637;N:150	76		10233215	6828213	6979097	10437637	150	SRX6854739	SRS5392941	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.79781		0.43575		0.96185		0.61011		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54367	54367	SRR10126089	SRX6854738	SRS5392940	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON16 01 H10	GSM4080975	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.310093893429947	ON16 01 H10	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.310093893429947	GSM4080975	GSM4080975: ON16 01 H10; Danio rerio; RNA Seq	GSM4080975		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080975	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22282_ON16_01_H10_mod.bam	bam	48896424.0	643374.0	GSM4080975 r1	0:76	A:14455624;C:9692935;G:9968124;T:14779517;N:224	76		14455624	9692935	9968124	14779517	224	SRX6854738	SRS5392940	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.81285		0.3318		0.95836		0.53689		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54368	54368	SRR10126088	SRX6854737	SRS5392939	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		ON12 01 D10	GSM4080974	tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.276868947734128	ON12 01 D10	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.276868947734128	GSM4080974	GSM4080974: ON12 01 D10; Danio rerio; RNA Seq	GSM4080974		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080974	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L22278_ON12_01_D10_mod.bam	bam	37841616.0	497916.0	GSM4080974 r1	0:76	A:10647168;C:8108969;G:8204459;T:10880848;N:172	76		10647168	8108969	8204459	10880848	172	SRX6854737	SRS5392939	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.83203		0.31484		0.953		0.51363		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54369	54369	SRR10126159	SRX6854736	SRS5392938	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 G04	GSM4081045	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.598622388793024	NBN 1 01 G04	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.598622388793024	GSM4081045	GSM4081045: NBN 1 01 G04; Danio rerio; RNA Seq	GSM4081045		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081045	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23857_NBN_1_01_G04_mod.bam	bam	32006260.0	421135.0	GSM4081045 r1	0:76	A:8610883;C:7464632;G:7494909;T:8435692;N:144	76		8610883	7464632	7494909	8435692	144	SRX6854736	SRS5392938	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.84284		0.06821		0.97331		0.50003		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54370	54370	SRR10126158	SRX6854735	SRS5392937	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 D06	GSM4081044	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.472262681006012	NBN 1 01 D06	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.472262681006012	GSM4081044	GSM4081044: NBN 1 01 D06; Danio rerio; RNA Seq	GSM4081044		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081044	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23870_NBN_1_01_D06_mod.bam	bam	17948388.0	236163.0	GSM4081044 r1	0:76	A:5102234;C:3980009;G:4032598;T:4833465;N:82	76		5102234	3980009	4032598	4833465	82	SRX6854735	SRS5392937	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.78433		0.1433		0.96895		0.48146		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54371	54371	SRR10126157	SRX6854734	SRS5392936	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 C06	GSM4081043	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.599218631820245	NBN 1 01 C06	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.599218631820245	GSM4081043	GSM4081043: NBN 1 01 C06; Danio rerio; RNA Seq	GSM4081043		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081043	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23869_NBN_1_01_C06_mod.bam	bam	26120972.0	343697.0	GSM4081043 r1	0:76	A:7285303;C:5839989;G:5890965;T:7104599;N:116	76		7285303	5839989	5890965	7104599	116	SRX6854734	SRS5392936	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.82402		0.12575		0.96197		0.52537		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54372	54372	SRR10126156	SRX6854733	SRS5392935	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 B06	GSM4081042	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.532356598173024	NBN 1 01 B06	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.532356598173024	GSM4081042	GSM4081042: NBN 1 01 B06; Danio rerio; RNA Seq	GSM4081042		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081042	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23868_NBN_1_01_B06_mod.bam	bam	21147912.0	278262.0	GSM4081042 r1	0:76	A:6114562;C:4550647;G:4607053;T:5875555;N:95	76		6114562	4550647	4607053	5875555	95	SRX6854733	SRS5392935	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.80519		0.21215		0.95189		0.49894		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54373	54373	SRR10126155	SRX6854732	SRS5392934	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 C07	GSM4081041	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.60565107325563	NBN 1 01 C07	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.60565107325563	GSM4081041	GSM4081041: NBN 1 01 C07; Danio rerio; RNA Seq	GSM4081041		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081041	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23877_NBN_1_01_C07_mod.bam	bam	17287644.0	227469.0	GSM4081041 r1	0:76	A:4734834;C:3930876;G:3976071;T:4645789;N:74	76		4734834	3930876	3976071	4645789	74	SRX6854732	SRS5392934	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.86762		0.10597		0.96613		0.50147		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54374	54374	SRR10126154	SRX6854731	SRS5392933	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 H04	GSM4081040	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.652633269764681	NBN 1 01 H04	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.652633269764681	GSM4081040	GSM4081040: NBN 1 01 H04; Danio rerio; RNA Seq	GSM4081040		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081040	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23858_NBN_1_01_H04_mod.bam	bam	48253160.0	634910.0	GSM4081040 r1	0:76	A:13424063;C:10616166;G:10721823;T:13490887;N:221	76		13424063	10616166	10721823	13490887	221	SRX6854731	SRS5392933	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.8954		0.17409		0.92884		0.49388		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54375	54375	SRR10126153	SRX6854730	SRS5392932	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 E06	GSM4081039	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.511207049654726	NBN 1 01 E06	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.511207049654726	GSM4081039	GSM4081039: NBN 1 01 E06; Danio rerio; RNA Seq	GSM4081039		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081039	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23871_NBN_1_01_E06_mod.bam	bam	29097056.0	382856.0	GSM4081039 r1	0:76	A:8234827;C:6362925;G:6406573;T:8092579;N:152	76		8234827	6362925	6406573	8092579	152	SRX6854730	SRS5392932	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.86249		0.26512		0.94608		0.48992		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54376	54376	SRR10126152	SRX6854729	SRS5392931	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 H06	GSM4081038	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.568841409012561	NBN 1 01 H06	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.568841409012561	GSM4081038	GSM4081038: NBN 1 01 H06; Danio rerio; RNA Seq	GSM4081038		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081038	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23874_NBN_1_01_H06_mod.bam	bam	32537044.0	428119.0	GSM4081038 r1	0:76	A:8987726;C:7310607;G:7366703;T:8871862;N:146	76		8987726	7310607	7366703	8871862	146	SRX6854729	SRS5392931	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.84497		0.16471		0.94351		0.50267		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54377	54377	SRR10126151	SRX6854728	SRS5392930	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 G06	GSM4081037	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.624181209060453	NBN 1 01 G06	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.624181209060453	GSM4081037	GSM4081037: NBN 1 01 G06; Danio rerio; RNA Seq	GSM4081037		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081037	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23873_NBN_1_01_G06_mod.bam	bam	12155364.0	159939.0	GSM4081037 r1	0:76	A:3344683;C:2708218;G:2783378;T:3319046;N:39	76		3344683	2708218	2783378	3319046	39	SRX6854728	SRS5392930	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.89597		0.11595		0.95306		0.46511		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54378	54378	SRR10126150	SRX6854727	SRS5392929	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 A07	GSM4081036	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.51658557940085	NBN 1 01 A07	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.51658557940085	GSM4081036	GSM4081036: NBN 1 01 A07; Danio rerio; RNA Seq	GSM4081036		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081036	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23875_NBN_1_01_A07_mod.bam	bam	30545692.0	401917.0	GSM4081036 r1	0:76	A:8429583;C:6966930;G:7076371;T:8072681;N:127	76		8429583	6966930	7076371	8072681	127	SRX6854727	SRS5392929	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.79087		0.10941		0.9656		0.51011		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54379	54379	SRR10126149	SRX6854726	SRS5392928	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 F06	GSM4081035	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.441816595438718	NBN 1 01 F06	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.441816595438718	GSM4081035	GSM4081035: NBN 1 01 F06; Danio rerio; RNA Seq	GSM4081035		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081035	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23872_NBN_1_01_F06_mod.bam	bam	18806276.0	247451.0	GSM4081035 r1	0:76	A:5151100;C:4382351;G:4395758;T:4876959;N:108	76		5151100	4382351	4395758	4876959	108	SRX6854726	SRS5392928	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.79771		0.10914		0.97417		0.46337		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54380	54380	SRR10126148	SRX6854725	SRS5392927	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 A05	GSM4081034	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.623421981847154	NBN 1 01 A05	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.623421981847154	GSM4081034	GSM4081034: NBN 1 01 A05; Danio rerio; RNA Seq	GSM4081034		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081034	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23859_NBN_1_01_A05_mod.bam	bam	45494588.0	598613.0	GSM4081034 r1	0:76	A:12663962;C:10058009;G:10243997;T:12528371;N:249	76		12663962	10058009	10243997	12528371	249	SRX6854725	SRS5392927	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87452		0.12669		0.96439		0.51002		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54381	54381	SRR10126147	SRX6854724	SRS5392926	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 D07	GSM4081033	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.67121387283237	NBN 1 01 D07	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.67121387283237	GSM4081033	GSM4081033: NBN 1 01 D07; Danio rerio; RNA Seq	GSM4081033		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081033	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23878_NBN_1_01_D07_mod.bam	bam	31553604.0	415179.0	GSM4081033 r1	0:76	A:8714681;C:7062201;G:7131427;T:8645143;N:152	76		8714681	7062201	7131427	8645143	152	SRX6854724	SRS5392926	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.8803		0.14617		0.94854		0.50368		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54382	54382	SRR10126146	SRX6854723	SRS5392925	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 E07	GSM4081032	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.594353386522259	NBN 1 01 E07	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.594353386522259	GSM4081032	GSM4081032: NBN 1 01 E07; Danio rerio; RNA Seq	GSM4081032		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081032	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23879_NBN_1_01_E07_mod.bam	bam	23124824.0	304274.0	GSM4081032 r1	0:76	A:6264129;C:5330640;G:5386597;T:6143334;N:124	76		6264129	5330640	5386597	6143334	124	SRX6854723	SRS5392925	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.8456		0.10134		0.97072		0.50122		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54383	54383	SRR10126145	SRX6854722	SRS5392924	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 B07	GSM4081031	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.621934520586096	NBN 1 01 B07	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.621934520586096	GSM4081031	GSM4081031: NBN 1 01 B07; Danio rerio; RNA Seq	GSM4081031		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081031	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23876_NBN_1_01_B07_mod.bam	bam	19638324.0	258399.0	GSM4081031 r1	0:76	A:5518210;C:4339448;G:4434264;T:5346306;N:96	76		5518210	4339448	4434264	5346306	96	SRX6854722	SRS5392924	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.89204		0.1016		0.96865		0.48751		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54384	54384	SRR10126144	SRX6854721	SRS5392923	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 A06	GSM4081030	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.555614689940042	NBN 1 01 A06	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.555614689940042	GSM4081030	GSM4081030: NBN 1 01 A06; Danio rerio; RNA Seq	GSM4081030		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081030	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23867_NBN_1_01_A06_mod.bam	bam	31688656.0	416956.0	GSM4081030 r1	0:76	A:8992439;C:6908404;G:7064869;T:8722777;N:167	76		8992439	6908404	7064869	8722777	167	SRX6854721	SRS5392923	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.84889		0.13507		0.9781		0.47411		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54385	54385	SRR10126143	SRX6854720	SRS5392922	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 1 01 D04	GSM4081029	tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.283621073701812	RG 1 01 D04	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.283621073701812	GSM4081029	GSM4081029: RG 1 01 D04; Danio rerio; RNA Seq	GSM4081029		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081029	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23854_RG_1_01_D04.bam	bam	12453588.0	163863.0	GSM4081029 r1	0:76	A:3624666;C:2746733;G:2769149;T:3312993;N:47	76		3624666	2746733	2769149	3312993	47	SRX6854720	SRS5392922	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.55387		0.08776		0.99531		0.77642		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54386	54386	SRR10126142	SRX6854719	SRS5392921	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 F04	GSM4081028	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.605363358887721	NBN 1 01 F04	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.605363358887721	GSM4081028	GSM4081028: NBN 1 01 F04; Danio rerio; RNA Seq	GSM4081028		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081028	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23856_NBN_1_01_F04_mod.bam	bam	29777712.0	391812.0	GSM4081028 r1	0:76	A:8287380;C:6634583;G:6702315;T:8153300;N:134	76		8287380	6634583	6702315	8153300	134	SRX6854719	SRS5392921	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.84681		0.14822		0.95899		0.48218		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54387	54387	SRR10126141	SRX6854718	SRS5392920	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 E04	GSM4081027	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.609232186919727	NBN 1 01 E04	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.609232186919727	GSM4081027	GSM4081027: NBN 1 01 E04; Danio rerio; RNA Seq	GSM4081027		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081027	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23855_NBN_1_01_E04_mod.bam	bam	27378468.0	360243.0	GSM4081027 r1	0:76	A:7514685;C:6210573;G:6248622;T:7404451;N:137	76		7514685	6210573	6248622	7404451	137	SRX6854718	SRS5392920	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87187		0.14148		0.95976		0.50299		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54388	54388	SRR10126140	SRX6854717	SRS5392919	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 1 01 C04	GSM4081026	tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.00268022023117434	RG 1 01 C04	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.00268022023117434	GSM4081026	GSM4081026: RG 1 01 C04; Danio rerio; RNA Seq	GSM4081026		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081026	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23853_RG_1_01_C04.bam	bam	17779136.0	233936.0	GSM4081026 r1	0:76	A:4924836;C:3601615;G:4002066;T:5250537;N:82	76		4924836	3601615	4002066	5250537	82	SRX6854717	SRS5392919	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.0068		0.00479		0.99924		0.7546		76		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54389	54389	SRR10126139	SRX6854716	SRS5392918	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 B05	GSM4081025	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.621158949173434	NBN 1 01 B05	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.621158949173434	GSM4081025	GSM4081025: NBN 1 01 B05; Danio rerio; RNA Seq	GSM4081025		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081025	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23860_NBN_1_01_B05_mod.bam	bam	23794460.0	313085.0	GSM4081025 r1	0:76	A:6486952;C:5421381;G:5559483;T:6326529;N:115	76		6486952	5421381	5559483	6326529	115	SRX6854716	SRS5392918	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.88749		0.09927		0.97167		0.51464		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54390	54390	SRR10126138	SRX6854715	SRS5392917	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 F05	GSM4081024	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.64362181199638	NBN 1 01 F05	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.64362181199638	GSM4081024	GSM4081024: NBN 1 01 F05; Danio rerio; RNA Seq	GSM4081024		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081024	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23864_NBN_1_01_F05_mod.bam	bam	34841136.0	458436.0	GSM4081024 r1	0:76	A:9468415;C:7931856;G:8068046;T:9372618;N:201	76		9468415	7931856	8068046	9372618	201	SRX6854715	SRS5392917	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.89991		0.09645		0.9612		0.50107		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54391	54391	SRR10126137	SRX6854714	SRS5392916	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 1 01 B04	GSM4081023	tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.0618454523025616	RG 1 01 B04	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.0618454523025616	GSM4081023	GSM4081023: RG 1 01 B04; Danio rerio; RNA Seq	GSM4081023		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081023	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23852_RG_1_01_B04.bam	bam	17866536.0	235086.0	GSM4081023 r1	0:76	A:5812722;C:3360958;G:3602639;T:5090127;N:90	76		5812722	3360958	3602639	5090127	90	SRX6854714	SRS5392916	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.17133		0.06449		0.99898		0.84014		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54392	54392	SRR10126136	SRX6854713	SRS5392915	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 1 01 E05	GSM4081022	tissue:Brain\|sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.613943437547748	NBN 1 01 E05	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.613943437547748	GSM4081022	GSM4081022: NBN 1 01 E05; Danio rerio; RNA Seq	GSM4081022		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081022	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23863_NBN_1_01_E05_mod.bam	bam	20887840.0	274840.0	GSM4081022 r1	0:76	A:5698091;C:4760347;G:4878634;T:5550655;N:113	76		5698091	4760347	4878634	5550655	113	SRX6854713	SRS5392915	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.86848		0.10705		0.96698		0.51406		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54393	54393	SRR10126303	SRX6854712	SRS5392914	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 4 03 G02	GSM4081189	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.396319736087877	NBN 4 03 G02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.396319736087877	GSM4081189	GSM4081189: NBN 4 03 G02; Danio rerio; RNA Seq	GSM4081189		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081189	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24033_NBN_4_03_G02_mod.bam	bam	32481184.0	427384.0	GSM4081189 r1	0:76	A:8891977;C:7560196;G:7559085;T:8469795;N:131	76		8891977	7560196	7559085	8469795	131	SRX6854712	SRS5392914	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.78442		0.1628		0.97847		0.47401		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54394	54394	SRR10126302	SRX6854711	SRS5392913	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 4 03 F02	GSM4081188	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.419934962554198	NBN 4 03 F02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.419934962554198	GSM4081188	GSM4081188: NBN 4 03 F02; Danio rerio; RNA Seq	GSM4081188		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081188	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24032_NBN_4_03_F02_mod.bam	bam	40102160.0	527660.0	GSM4081188 r1	0:76	A:10964163;C:9350144;G:9306636;T:10480993;N:224	76		10964163	9350144	9306636	10480993	224	SRX6854711	SRS5392913	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.78826		0.16336		0.97252		0.48219		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54395	54395	SRR10126301	SRX6854710	SRS5392912	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 03 G01	GSM4081187	tissue:Brain\|sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.245253335273735	RG 4 03 G01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.245253335273735	GSM4081187	GSM4081187: RG 4 03 G01; Danio rerio; RNA Seq	GSM4081187		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081187	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24025_RG_4_03_G01_mod.bam	bam	30288280.0	398530.0	GSM4081187 r1	0:76	A:8102225;C:7392718;G:7404963;T:7388259;N:115	76		8102225	7392718	7404963	7388259	115	SRX6854710	SRS5392912	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.58611		0.06211		0.99095		0.56894		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54396	54396	SRR10126300	SRX6854709	SRS5392911	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 03 H01	GSM4081186	tissue:Brain\|sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.540783502310504	RG 4 03 H01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.540783502310504	GSM4081186	GSM4081186: RG 4 03 H01; Danio rerio; RNA Seq	GSM4081186		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081186	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24026_RG_4_03_H01_mod.bam	bam	55086776.0	724826.0	GSM4081186 r1	0:76	A:15030228;C:12501198;G:12598562;T:14956486;N:302	76		15030228	12501198	12598562	14956486	302	SRX6854709	SRS5392911	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.80615		0.13988		0.95765		0.48086		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54397	54397	SRR10126299	SRX6854708	SRS5392910	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 03 E01	GSM4081185	tissue:Brain\|sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.0637304637280315	RG 4 03 E01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.0637304637280315	GSM4081185	GSM4081185: RG 4 03 E01; Danio rerio; RNA Seq	GSM4081185		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081185	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24023_RG_4_03_E01.bam	bam	43745296.0	575596.0	GSM4081185 r1	0:76	A:11664185;C:10975964;G:10921062;T:10183883;N:202	76		11664185	10975964	10921062	10183883	202	SRX6854708	SRS5392910	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.25729		0.10073		0.99813		0.85282		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54398	54398	SRR10126298	SRX6854707	SRS5392909	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 03 D01	GSM4081184	tissue:Brain\|sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.569502699214683	RG 4 03 D01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.569502699214683	GSM4081184	GSM4081184: RG 4 03 D01; Danio rerio; RNA Seq	GSM4081184		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081184	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24022_RG_4_03_D01_mod.bam	bam	45673416.0	600966.0	GSM4081184 r1	0:76	A:12261353;C:10688092;G:10675712;T:12047986;N:273	76		12261353	10688092	10675712	12047986	273	SRX6854707	SRS5392909	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.83933		0.08001		0.9653		0.48949		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54399	54399	SRR10126297	SRX6854706	SRS5392908	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 03 F01	GSM4081183	tissue:Brain\|sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.0898847052989515	RG 4 03 F01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.0898847052989515	GSM4081183	GSM4081183: RG 4 03 F01; Danio rerio; RNA Seq	GSM4081183		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081183	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24024_RG_4_03_F01_mod.bam	bam	51495092.0	677567.0	GSM4081183 r1	0:76	A:13725202;C:12850216;G:12784293;T:12135098;N:283	76		13725202	12850216	12784293	12135098	283	SRX6854706	SRS5392908	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.33847		0.15231		0.99845		0.68863		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54400	54400	SRR10126296	SRX6854705	SRS5392907	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 03 C01	GSM4081182	tissue:Brain\|sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.155483476006256	RG 4 03 C01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.155483476006256	GSM4081182	GSM4081182: RG 4 03 C01; Danio rerio; RNA Seq	GSM4081182		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081182	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24021_RG_4_03_C01.bam	bam	29546368.0	388768.0	GSM4081182 r1	0:76	A:8324657;C:6832651;G:6875775;T:7513152;N:133	76		8324657	6832651	6875775	7513152	133	SRX6854705	SRS5392907	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.43383		0.15437		0.99634		0.49243		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54401	54401	SRR10126295	SRX6854704	SRS5392906	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 03 B01	GSM4081181	tissue:Brain\|sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.615303809854487	RG 4 03 B01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.615303809854487	GSM4081181	GSM4081181: RG 4 03 B01; Danio rerio; RNA Seq	GSM4081181		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081181	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24020_RG_4_03_B01_mod.bam	bam	60175432.0	791782.0	GSM4081181 r1	0:76	A:16514318;C:13627412;G:13665406;T:16368047;N:249	76		16514318	13627412	13665406	16368047	249	SRX6854704	SRS5392906	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.85908		0.10782		0.96148		0.51361		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54402	54402	SRR10126294	SRX6854703	SRS5392905	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 03 A01	GSM4081180	tissue:Brain\|sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.570142657011503	RG 4 03 A01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.570142657011503	GSM4081180	GSM4081180: RG 4 03 A01; Danio rerio; RNA Seq	GSM4081180		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081180	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24019_RG_4_03_A01_mod.bam	bam	38510568.0	506718.0	GSM4081180 r1	0:76	A:10747250;C:8632416;G:8694972;T:10435736;N:194	76		10747250	8632416	8694972	10435736	194	SRX6854703	SRS5392905	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.852		0.11594		0.96924		0.4745		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54403	54403	SRR10126293	SRX6854702	SRS5392903	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 B12	GSM4081179	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.428431953922818	RG 4 02 B12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.428431953922818	GSM4081179	GSM4081179: RG 4 02 B12; Danio rerio; RNA Seq	GSM4081179		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081179	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24012_RG_4_02_B12_mod.bam	bam	23196948.0	305223.0	GSM4081179 r1	0:76	A:6650835;C:5125890;G:5156953;T:6263179;N:91	76		6650835	5125890	5156953	6263179	91	SRX6854702	SRS5392903	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.68027		0.08335		0.99541		0.78262		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54404	54404	SRR10126292	SRX6854701	SRS5392904	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 C12	GSM4081178	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.256314554078489	RG 4 02 C12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.256314554078489	GSM4081178	GSM4081178: RG 4 02 C12; Danio rerio; RNA Seq	GSM4081178		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081178	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24013_RG_4_02_C12.bam	bam	20301196.0	267121.0	GSM4081178 r1	0:76	A:5819263;C:4507058;G:4523322;T:5451458;N:95	76		5819263	4507058	4523322	5451458	95	SRX6854701	SRS5392904	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.50417		0.05837		0.9988		0.96684		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54405	54405	SRR10126291	SRX6854700	SRS5392902	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 D12	GSM4081177	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.491189003992584	RG 4 02 D12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.491189003992584	GSM4081177	GSM4081177: RG 4 02 D12; Danio rerio; RNA Seq	GSM4081177		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081177	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24014_RG_4_02_D12_mod.bam	bam	52577256.0	691806.0	GSM4081177 r1	0:76	A:14408204;C:11925559;G:11938551;T:14304703;N:239	76		14408204	11925559	11938551	14304703	239	SRX6854700	SRS5392902	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.80575		0.1619		0.96516		0.46709		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54406	54406	SRR10126290	SRX6854699	SRS5392901	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 A12	GSM4081176	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.374689047966583	RG 4 02 A12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.374689047966583	GSM4081176	GSM4081176: RG 4 02 A12; Danio rerio; RNA Seq	GSM4081176		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081176	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24011_RG_4_02_A12_mod.bam	bam	24470556.0	321981.0	GSM4081176 r1	0:76	A:6855056;C:5618406;G:5599835;T:6397133;N:126	76		6855056	5618406	5599835	6397133	126	SRX6854699	SRS5392901	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.64203		0.08348		0.99334		0.65535		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54407	54407	SRR10126289	SRX6854698	SRS5392900	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 H11	GSM4081175	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.0753273689206053	RG 4 02 H11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.0753273689206053	GSM4081175	GSM4081175: RG 4 02 H11; Danio rerio; RNA Seq	GSM4081175		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081175	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24010_RG_4_02_H11.bam	bam	21619340.0	284465.0	GSM4081175 r1	0:76	A:5849729;C:5318056;G:5286321;T:5165140;N:94	76		5849729	5318056	5286321	5165140	94	SRX6854698	SRS5392900	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.26022		0.12088		0.99874		0.73088		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54408	54408	SRR10126288	SRX6854697	SRS5392899	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 G11	GSM4081174	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.454699812270569	RG 4 02 G11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.454699812270569	GSM4081174	GSM4081174: RG 4 02 G11; Danio rerio; RNA Seq	GSM4081174		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081174	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24009_RG_4_02_G11_mod.bam	bam	25422228.0	334503.0	GSM4081174 r1	0:76	A:6982673;C:5930126;G:5939036;T:6570320;N:73	76		6982673	5930126	5939036	6570320	73	SRX6854697	SRS5392899	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.74275		0.06432		0.98723		0.57598		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54409	54409	SRR10126287	SRX6854696	SRS5392898	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 G12	GSM4081173	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.584411223876839	RG 4 02 G12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.584411223876839	GSM4081173	GSM4081173: RG 4 02 G12; Danio rerio; RNA Seq	GSM4081173		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081173	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24017_RG_4_02_G12_mod.bam	bam	57923932.0	762157.0	GSM4081173 r1	0:76	A:15942052;C:13000252;G:13080471;T:15900882;N:275	76		15942052	13000252	13080471	15900882	275	SRX6854696	SRS5392898	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.81908		0.11496		0.95735		0.50954		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54410	54410	SRR10126286	SRX6854695	SRS5392897	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 F12	GSM4081172	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.320746896029119	RG 4 02 F12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.320746896029119	GSM4081172	GSM4081172: RG 4 02 F12; Danio rerio; RNA Seq	GSM4081172		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081172	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24016_RG_4_02_F12.bam	bam	23468648.0	308798.0	GSM4081172 r1	0:76	A:7319180;C:4363209;G:4610283;T:7175855;N:121	76		7319180	4363209	4610283	7175855	121	SRX6854695	SRS5392897	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.55485		0.12886		0.99872		0.98508		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54411	54411	SRR10126285	SRX6854694	SRS5392896	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 E12	GSM4081171	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.588827526294561	RG 4 02 E12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.588827526294561	GSM4081171	GSM4081171: RG 4 02 E12; Danio rerio; RNA Seq	GSM4081171		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081171	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24015_RG_4_02_E12_mod.bam	bam	58770876.0	773301.0	GSM4081171 r1	0:76	A:16791138;C:12494383;G:12618663;T:16866357;N:335	76		16791138	12494383	12618663	16866357	335	SRX6854694	SRS5392896	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.85803		0.2024		0.9583		0.56471		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54412	54412	SRR10126284	SRX6854693	SRS5392895	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 F11	GSM4081170	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.324106247522213	RG 4 02 F11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.324106247522213	GSM4081170	GSM4081170: RG 4 02 F11; Danio rerio; RNA Seq	GSM4081170		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081170	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24008_RG_4_02_F11.bam	bam	29330604.0	385929.0	GSM4081170 r1	0:76	A:8485315;C:6315690;G:6498851;T:8030598;N:150	76		8485315	6315690	6498851	8030598	150	SRX6854693	SRS5392895	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.6157		0.0926		0.99677		0.62475		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54413	54413	SRR10126283	SRX6854692	SRS5392894	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 E11	GSM4081169	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.580370132771242	RG 4 02 E11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.580370132771242	GSM4081169	GSM4081169: RG 4 02 E11; Danio rerio; RNA Seq	GSM4081169		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081169	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24007_RG_4_02_E11_mod.bam	bam	53053700.0	698075.0	GSM4081169 r1	0:76	A:14361081;C:12184584;G:12231766;T:14275990;N:279	76		14361081	12184584	12231766	14275990	279	SRX6854692	SRS5392894	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87764		0.1324		0.97137		0.48975		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54414	54414	SRR10126282	SRX6854691	SRS5392893	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 D11	GSM4081168	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.175915507364975	RG 4 02 D11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.175915507364975	GSM4081168	GSM4081168: RG 4 02 D11; Danio rerio; RNA Seq	GSM4081168		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081168	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24006_RG_4_02_D11.bam	bam	26747136.0	351936.0	GSM4081168 r1	0:76	A:7566075;C:6116368;G:6185399;T:6879178;N:116	76		7566075	6116368	6185399	6879178	116	SRX6854691	SRS5392893	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.4582		0.13972		0.99839		0.60869		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54415	54415	SRR10126281	SRX6854690	SRS5392892	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 H12	GSM4081167	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.641571006115169	RG 4 02 H12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.641571006115169	GSM4081167	GSM4081167: RG 4 02 H12; Danio rerio; RNA Seq	GSM4081167		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081167	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24018_RG_4_02_H12_mod.bam	bam	61286476.0	806401.0	GSM4081167 r1	0:76	A:16910460;C:13631719;G:13724446;T:17019529;N:322	76		16910460	13631719	13724446	17019529	322	SRX6854690	SRS5392892	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87214		0.11436		0.95946		0.47007		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54416	54416	SRR10126280	SRX6854689	SRS5392890	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 C11	GSM4081166	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.38192650803246	RG 4 02 C11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.38192650803246	GSM4081166	GSM4081166: RG 4 02 C11; Danio rerio; RNA Seq	GSM4081166		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081166	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24005_RG_4_02_C11.bam	bam	16595664.0	218364.0	GSM4081166 r1	0:76	A:4663104;C:3733046;G:3788322;T:4411110;N:82	76		4663104	3733046	3788322	4411110	82	SRX6854689	SRS5392890	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.63386		0.12677		0.9974		0.39862		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54417	54417	SRR10126079	SRX6854688	SRS5392891	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 F12	GSM4081273	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.525010889856876	NBN 5 03 F12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.525010889856876	GSM4081273	GSM4081273: NBN 5 03 F12; Danio rerio; RNA Seq	GSM4081273		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081273	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24112_NBN_5_03_F12_mod.bam	bam	48823084.0	642409.0	GSM4081273 r1	0:76	A:13281310;C:11283844;G:11320552;T:12937124;N:254	76		13281310	11283844	11320552	12937124	254	SRX6854688	SRS5392891	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.84855		0.12882		0.97011		0.5031		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54418	54418	SRR10126078	SRX6854687	SRS5392889	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 E12	GSM4081272	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.58888053902187	NBN 5 03 E12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.58888053902187	GSM4081272	GSM4081272: NBN 5 03 E12; Danio rerio; RNA Seq	GSM4081272		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081272	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24111_NBN_5_03_E12_mod.bam	bam	53368568.0	702218.0	GSM4081272 r1	0:76	A:14305398;C:12420925;G:12495590;T:14146395;N:260	76		14305398	12420925	12495590	14146395	260	SRX6854687	SRS5392889	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.88543		0.10092		0.96493		0.51049		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54419	54419	SRR10126077	SRX6854686	SRS5392888	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 H12	GSM4081271	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.676307655192171	NBN 5 03 H12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.676307655192171	GSM4081271	GSM4081271: NBN 5 03 H12; Danio rerio; RNA Seq	GSM4081271		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081271	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24114_NBN_5_03_H12_mod.bam	bam	50399780.0	663155.0	GSM4081271 r1	0:76	A:14087482;C:11098672;G:11185255;T:14028118;N:253	76		14087482	11098672	11185255	14028118	253	SRX6854686	SRS5392888	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.89616		0.14239		0.93754		0.488		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54420	54420	SRR10126076	SRX6854685	SRS5392887	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 G12	GSM4081270	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.469570262254911	NBN 5 03 G12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.469570262254911	GSM4081270	GSM4081270: NBN 5 03 G12; Danio rerio; RNA Seq	GSM4081270		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081270	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24113_NBN_5_03_G12_mod.bam	bam	39821416.0	523966.0	GSM4081270 r1	0:76	A:11006563;C:9116301;G:9155476;T:10542886;N:190	76		11006563	9116301	9155476	10542886	190	SRX6854685	SRS5392887	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.79523		0.15323		0.97794		0.4983		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54421	54421	SRR10126075	SRX6854684	SRS5392886	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 B12	GSM4081269	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.606668639243757	NBN 5 03 B12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.606668639243757	GSM4081269	GSM4081269: NBN 5 03 B12; Danio rerio; RNA Seq	GSM4081269		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081269	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24108_NBN_5_03_B12_mod.bam	bam	49564996.0	652171.0	GSM4081269 r1	0:76	A:13457686;C:11463971;G:11462445;T:13180670;N:224	76		13457686	11463971	11462445	13180670	224	SRX6854684	SRS5392886	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.8526		0.10679		0.95647		0.47783		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54422	54422	SRR10126074	SRX6854683	SRS5392885	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 C12	GSM4081268	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.504928000361481	NBN 5 03 C12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.504928000361481	GSM4081268	GSM4081268: NBN 5 03 C12; Danio rerio; RNA Seq	GSM4081268		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081268	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24109_NBN_5_03_C12_mod.bam	bam	53799868.0	707893.0	GSM4081268 r1	0:76	A:14477673;C:12676492;G:12642373;T:14003009;N:321	76		14477673	12676492	12642373	14003009	321	SRX6854683	SRS5392885	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.83364		0.12094		0.96607		0.50035		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54423	54423	SRR10126073	SRX6854682	SRS5392884	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 D12	GSM4081267	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.580831314940795	NBN 5 03 D12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.580831314940795	GSM4081267	GSM4081267: NBN 5 03 D12; Danio rerio; RNA Seq	GSM4081267		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081267	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24110_NBN_5_03_D12_mod.bam	bam	62659492.0	824467.0	GSM4081267 r1	0:76	A:17501184;C:13903981;G:13981600;T:17272412;N:315	76		17501184	13903981	13981600	17272412	315	SRX6854682	SRS5392884	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.84637		0.16833		0.94176		0.51092		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54424	54424	SRR10126072	SRX6854681	SRS5392883	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 A12	GSM4081266	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.601561083260848	NBN 5 03 A12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.601561083260848	GSM4081266	GSM4081266: NBN 5 03 A12; Danio rerio; RNA Seq	GSM4081266		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081266	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24107_NBN_5_03_A12_mod.bam	bam	49451984.0	650684.0	GSM4081266 r1	0:76	A:13859171;C:10940822;G:10987740;T:13664031;N:220	76		13859171	10940822	10987740	13664031	220	SRX6854681	SRS5392883	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87251		0.1665		0.94491		0.48105		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54425	54425	SRR10126071	SRX6854680	SRS5392882	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 H11	GSM4081265	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.55113188683118	NBN 5 03 H11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.55113188683118	GSM4081265	GSM4081265: NBN 5 03 H11; Danio rerio; RNA Seq	GSM4081265		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081265	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24106_NBN_5_03_H11_mod.bam	bam	45911372.0	604097.0	GSM4081265 r1	0:76	A:12937055;C:10127940;G:10124771;T:12721382;N:224	76		12937055	10127940	10124771	12721382	224	SRX6854680	SRS5392882	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.83064		0.18688		0.94038		0.48867		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54426	54426	SRR10126070	SRX6854679	SRS5392881	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 F11	GSM4081264	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.620118980345189	NBN 5 03 F11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.620118980345189	GSM4081264	GSM4081264: NBN 5 03 F11; Danio rerio; RNA Seq	GSM4081264		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081264	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24104_NBN_5_03_F11_mod.bam	bam	54050744.0	711194.0	GSM4081264 r1	0:76	A:14547427;C:12569309;G:12552401;T:14381328;N:279	76		14547427	12569309	12552401	14381328	279	SRX6854679	SRS5392881	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87911		0.10227		0.96745		0.50866		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54427	54427	SRR10126069	SRX6854678	SRS5392880	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 G11	GSM4081263	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.58316051570689	NBN 5 03 G11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.58316051570689	GSM4081263	GSM4081263: NBN 5 03 G11; Danio rerio; RNA Seq	GSM4081263		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081263	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24105_NBN_5_03_G11_mod.bam	bam	45086924.0	593249.0	GSM4081263 r1	0:76	A:12126030;C:10507396;G:10516536;T:11936751;N:211	76		12126030	10507396	10516536	11936751	211	SRX6854678	SRS5392880	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.8887		0.10291		0.95931		0.52124		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54428	54428	SRR10126068	SRX6854677	SRS5392879	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 5 03 E11	GSM4081262	tissue:Brain\|sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.623957668396341	NBN 5 03 E11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 03\|batch:bfx855\|fraction mapped:0.623957668396341	GSM4081262	GSM4081262: NBN 5 03 E11; Danio rerio; RNA Seq	GSM4081262		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081262	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24103_NBN_5_03_E11_mod.bam	bam	41548592.0	546692.0	GSM4081262 r1	0:76	A:11489533;C:9322886;G:9355670;T:11380355;N:148	76		11489533	9322886	9355670	11380355	148	SRX6854677	SRS5392879	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.88164		0.1585		0.95446		0.47372		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54429	54429	SRR10126279	SRX6854676	SRS5392877	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 3 02 D10	GSM4081165	tissue:Brain\|sorting:NBN\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.663327926186879	NBN 3 02 D10	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.663327926186879	GSM4081165	GSM4081165: NBN 3 02 D10; Danio rerio; RNA Seq	GSM4081165		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081165	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23998_NBN_3_02_D10_mod.bam	bam	47706872.0	627722.0	GSM4081165 r1	0:76	A:12877045;C:11012151;G:11040022;T:12777416;N:238	76		12877045	11012151	11040022	12777416	238	SRX6854676	SRS5392877	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.90053		0.11161		0.96885		0.4594		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54430	54430	SRR10126278	SRX6854675	SRS5392876	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 3 02 C10	GSM4081164	tissue:Brain\|sorting:NBN\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.656334748260818	NBN 3 02 C10	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.656334748260818	GSM4081164	GSM4081164: NBN 3 02 C10; Danio rerio; RNA Seq	GSM4081164		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081164	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23997_NBN_3_02_C10_mod.bam	bam	56686956.0	745881.0	GSM4081164 r1	0:76	A:15064775;C:13287109;G:13331184;T:15003602;N:286	76		15064775	13287109	13331184	15003602	286	SRX6854675	SRS5392876	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.9083		0.09079		0.96605		0.48736		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54431	54431	SRR10126277	SRX6854674	SRS5392878	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 3 02 F10	GSM4081163	tissue:Brain\|sorting:NBN\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.676356413825882	NBN 3 02 F10	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.676356413825882	GSM4081163	GSM4081163: NBN 3 02 F10; Danio rerio; RNA Seq	GSM4081163		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081163	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24000_NBN_3_02_F10_mod.bam	bam	56255124.0	740199.0	GSM4081163 r1	0:76	A:15090887;C:13028410;G:13078082;T:15057469;N:276	76		15090887	13028410	13078082	15057469	276	SRX6854674	SRS5392878	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.914		0.10217		0.95684		0.52388		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54432	54432	SRR10126276	SRX6854673	SRS5392875	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 G10	GSM4081162	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.622636514669279	RG 4 02 G10	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.622636514669279	GSM4081162	GSM4081162: RG 4 02 G10; Danio rerio; RNA Seq	GSM4081162		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081162	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24001_RG_4_02_G10_mod.bam	bam	24974740.0	328615.0	GSM4081162 r1	0:76	A:7027112;C:5576222;G:5635470;T:6735797;N:139	76		7027112	5576222	5635470	6735797	139	SRX6854673	SRS5392875	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.84236		0.05961		0.98472		0.57975		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54433	54433	SRR10126275	SRX6854672	SRS5392874	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		NBN 3 02 E10	GSM4081161	tissue:Brain\|sorting:NBN\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.64390443229931	NBN 3 02 E10	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:NBN\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.64390443229931	GSM4081161	GSM4081161: NBN 3 02 E10; Danio rerio; RNA Seq	GSM4081161		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081161	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L23999_NBN_3_02_E10_mod.bam	bam	55018300.0	723925.0	GSM4081161 r1	0:76	A:14695848;C:12861715;G:12903702;T:14556820;N:215	76		14695848	12861715	12903702	14556820	215	SRX6854672	SRS5392874	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.89892		0.1023		0.97256		0.53216		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54434	54434	SRR10126274	SRX6854671	SRS5392873	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 B11	GSM4081160	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.30622932370946	RG 4 02 B11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.30622932370946	GSM4081160	GSM4081160: RG 4 02 B11; Danio rerio; RNA Seq	GSM4081160		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081160	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24004_RG_4_02_B11_mod.bam	bam	39167284.0	515359.0	GSM4081160 r1	0:76	A:10957063;C:8804736;G:8822269;T:10582986;N:230	76		10957063	8804736	8822269	10582986	230	SRX6854671	SRS5392873	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.67676		0.25588		0.98709		0.63136		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54435	54435	SRR10126273	SRX6854670	SRS5392872	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain	pubmed:31908317		RG 4 02 A11	GSM4081159	tissue:Brain\|sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.602995851478063	RG 4 02 A11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	sorting:RG\|FISH id:bfx855 02\|batch:bfx855\|fraction mapped:0.602995851478063	GSM4081159	GSM4081159: RG 4 02 A11; Danio rerio; RNA Seq	GSM4081159		1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4081159	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784	intentional duplicate\|dangling references:treat as unmapped	L24003_RG_4_02_A11_mod.bam	bam	50119492.0	659467.0	GSM4081159 r1	0:76	A:13705061;C:11384188;G:11439379;T:13590614;N:250	76		13705061	11384188	11439379	13590614	250	SRX6854670	SRS5392872	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.84901		0.1277		0.95773		0.46374		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System

Advanced export

JSON shape: default, array, newline-delimited

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");;