metadata: run_metadata: 241 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and tissue

241 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and tissue_curation = "Head"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
19476	19476	ERR14208827	ERX13611047	ERS22979745	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	Scrambled 1 sample	SAMEA117628607	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 004\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 004\|scientific name:Danio rerio									Raw reads: Scrambled 1 sample	webin reads Scrambled 1 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: Scrambled 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F04.bam	bam	8497741.0	104283.0	webin reads Scrambled 1 sample	0:81.49	A:2628864;C:1112827;G:2146146;T:2609768;N:136	81		2628864	1112827	2146146	2609768	136	ERX13611047	ERS22979745	ERA31123309	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19477	19477	ERR14208813	ERX13611033	ERS22979748	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 1 sample	SAMEA117628610	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 007\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 007\|scientific name:Danio rerio									Raw reads: ythdf2KO 1 sample	webin reads ythdf2KO 1 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: ythdf2KO 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D09.bam	bam	673213184.0	8122011.0	webin reads ythdf2KO 1 sample	0:82.89	A:180836688;C:107076381;G:193711319;T:191586188;N:2608	82		180836688	107076381	193711319	191586188	2608	ERX13611033	ERS22979748	ERA31123295	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19478	19478	ERR14208811	ERX13611031	ERS22979755	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 6 sample	SAMEA117628617	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 014\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 014\|scientific name:Danio rerio									Raw reads: GFP 6 sample	webin reads GFP 6 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: GFP 6 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	H01.bam	bam	337553787.0	3153658.0	webin reads GFP 6 sample	0:107.04	A:81816649;C:55524538;G:113686171;T:86525390;N:1039	107		81816649	55524538	113686171	86525390	1039	ERX13611031	ERS22979755	ERA31123293	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19479	19479	ERR14208821	ERX13611041	ERS22979752	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 5 sample	SAMEA117628614	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 011\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 011\|scientific name:Danio rerio									Raw reads: ythdf2KO 5 sample	webin reads ythdf2KO 5 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: ythdf2KO 5 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G10.bam	bam	226771232.0	2050630.0	webin reads ythdf2KO 5 sample	0:110.59	A:56944731;C:30766256;G:83820146;T:55239221;N:878	110		56944731	30766256	83820146	55239221	878	ERX13611041	ERS22979752	ERA31123303	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19480	19480	ERR14208818	ERX13611038	ERS22979750	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 3 sample	SAMEA117628612	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 009\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 009\|scientific name:Danio rerio									Raw reads: ythdf2KO 3 sample	webin reads ythdf2KO 3 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: ythdf2KO 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G08.bam	bam	351425328.0	3771763.0	webin reads ythdf2KO 3 sample	0:93.17	A:83933175;C:50138103;G:128300798;T:89051913;N:1339	93		83933175	50138103	128300798	89051913	1339	ERX13611038	ERS22979750	ERA31123300	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19481	19481	ERR14208826	ERX13611046	ERS22979758	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	YTHDF2 3 sample	SAMEA117628620	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 017\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 017\|scientific name:Danio rerio									Raw reads: YTHDF2 3 sample	webin reads YTHDF2 3 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: YTHDF2 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	E01.bam	bam	181017083.0	1670383.0	webin reads YTHDF2 3 sample	0:108.37	A:38910474;C:31607688;G:67095095;T:43403227;N:599	108		38910474	31607688	67095095	43403227	599	ERX13611046	ERS22979758	ERA31123308	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19482	19482	ERR14208815	ERX13611035	ERS22979749	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 2 sample	SAMEA117628611	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 008\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 008\|scientific name:Danio rerio									Raw reads: ythdf2KO 2 sample	webin reads ythdf2KO 2 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: ythdf2KO 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D10.bam	bam	282414832.0	2675188.0	webin reads ythdf2KO 2 sample	0:105.57	A:73651155;C:41694223;G:96485766;T:70582706;N:982	105		73651155	41694223	96485766	70582706	982	ERX13611035	ERS22979749	ERA31123297	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19483	19483	ERR14208804	ERX13611024	ERS22979742	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 1 sample	SAMEA117628604	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 001\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 001\|scientific name:Danio rerio									Raw reads: GFP 1 sample	webin reads GFP 1 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: GFP 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F01.bam	bam	8036009.0	97716.0	webin reads GFP 1 sample	0:82.24	A:2445867;C:1074319;G:2086526;T:2429153;N:144	82		2445867	1074319	2086526	2429153	144	ERX13611024	ERS22979742	ERA31123286	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19484	19484	ERR14208829	ERX13611049	ERS22979747	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	Scrambled 3 sample	SAMEA117628609	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 006\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 006\|scientific name:Danio rerio									Raw reads: Scrambled 3 sample	webin reads Scrambled 3 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: Scrambled 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F06.bam	bam	90051514.0	910768.0	webin reads Scrambled 3 sample	0:98.87	A:30132090;C:13700682;G:16323331;T:29894332;N:1079	98		30132090	13700682	16323331	29894332	1079	ERX13611049	ERS22979747	ERA31123311	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19485	19485	ERR14208809	ERX13611029	ERS22979753	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 4 sample	SAMEA117628615	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 012\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 012\|scientific name:Danio rerio									Raw reads: GFP 4 sample	webin reads GFP 4 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: GFP 4 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G11.bam	bam	72278736.0	751207.0	webin reads GFP 4 sample	0:96.22	A:17589630;C:11153310;G:25212154;T:18323416;N:226	96		17589630	11153310	25212154	18323416	226	ERX13611029	ERS22979753	ERA31123291	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19486	19486	ERR14208806	ERX13611026	ERS22979743	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 2 sample	SAMEA117628605	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 002\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 002\|scientific name:Danio rerio									Raw reads: GFP 2 sample	webin reads GFP 2 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: GFP 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F02.bam	bam	19196592.0	230075.0	webin reads GFP 2 sample	0:83.44	A:5957309;C:2709511;G:4434875;T:6094552;N:345	83		5957309	2709511	4434875	6094552	345	ERX13611026	ERS22979743	ERA31123288	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19487	19487	ERR14208810	ERX13611030	ERS22979754	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 5 sample	SAMEA117628616	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 013\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 013\|scientific name:Danio rerio									Raw reads: GFP 5 sample	webin reads GFP 5 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: GFP 5 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G12.bam	bam	431708790.0	5173015.0	webin reads GFP 5 sample	0:83.45	A:119077902;C:68329173;G:126879243;T:117420803;N:1669	83		119077902	68329173	126879243	117420803	1669	ERX13611030	ERS22979754	ERA31123292	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19488	19488	ERR14208828	ERX13611048	ERS22979746	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	Scrambled 2 sample	SAMEA117628608	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 005\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 005\|scientific name:Danio rerio									Raw reads: Scrambled 2 sample	webin reads Scrambled 2 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: Scrambled 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F05.bam	bam	32695808.0	357320.0	webin reads Scrambled 2 sample	0:91.50	A:10989624;C:4719485;G:5954777;T:11031603;N:319	91		10989624	4719485	5954777	11031603	319	ERX13611048	ERS22979746	ERA31123310	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19489	19489	ERR14208819	ERX13611039	ERS22979751	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 4 sample	SAMEA117628613	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 010\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 010\|scientific name:Danio rerio									Raw reads: ythdf2KO 4 sample	webin reads ythdf2KO 4 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: ythdf2KO 4 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G09.bam	bam	254231539.0	2766205.0	webin reads ythdf2KO 4 sample	0:91.91	A:63984512;C:40328422;G:86431821;T:63485754;N:1030	91		63984512	40328422	86431821	63485754	1030	ERX13611039	ERS22979751	ERA31123301	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19490	19490	ERR14208808	ERX13611028	ERS22979744	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 3 sample	SAMEA117628606	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 003\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 003\|scientific name:Danio rerio									Raw reads: GFP 3 sample	webin reads GFP 3 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: GFP 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F03.bam	bam	35932988.0	419944.0	webin reads GFP 3 sample	0:85.57	A:11252929;C:5321445;G:8032297;T:11325814;N:503	85		11252929	5321445	8032297	11325814	503	ERX13611028	ERS22979744	ERA31123290	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19491	19491	ERR14208825	ERX13611045	ERS22979757	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	YTHDF2 2 sample	SAMEA117628619	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 016\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 016\|scientific name:Danio rerio									Raw reads: YTHDF2 2 sample	webin reads YTHDF2 2 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: YTHDF2 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D12.bam	bam	626993184.0	7599502.0	webin reads YTHDF2 2 sample	0:82.50	A:182701108;C:91008174;G:172822143;T:180459253;N:2506	82		182701108	91008174	172822143	180459253	2506	ERX13611045	ERS22979757	ERA31123307	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19492	19492	ERR14208822	ERX13611042	ERS22979756	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	YTHDF2 1 sample	SAMEA117628618	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 015\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 015\|scientific name:Danio rerio									Raw reads: YTHDF2 1 sample	webin reads YTHDF2 1 sample		unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP167299	Raw reads: YTHDF2 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D11.bam	bam	120748751.0	1368887.0	webin reads YTHDF2 1 sample	0:88.21	A:34957526;C:19985010;G:32927086;T:32878659;N:470	88		34957526	19985010	32927086	32878659	470	ERX13611042	ERS22979756	ERA31123304	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
32037	32037	SRR28992909	SRX24520261	SRS21267950	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Kcnd2 Wt1		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Kcnd2 Wt1\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: pools of isolated larval head	Kcnd2 Wt1	Kcnd2 Wt1	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Kcnd2_Wt1.fq.gz	fastq	3386455050.0	22576367.0	Kcnd2 Wt1.fq.gz	0:150	A:967137430;C:730108913;G:738646978;T:950549427;N:12302	150		967137430	730108913	738646978	950549427	12302	SRX24520261	SRS21267950	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32038	32038	SRR28992910	SRX24520260	SRS21267949	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Arfgef1 Hom3		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Arfgef1 Hom3\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: pools of isolated larval head	Arfgef1 Hom3	Arfgef1 Hom3	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Arfgef1_Hom3.fq.gz	fastq	3647365500.0	24315770.0	Arfgef1 Hom3.fq.gz	0:150	A:923919033;C:903440333;G:911845870;T:908147370;N:12894	150		923919033	903440333	911845870	908147370	12894	SRX24520260	SRS21267949	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32039	32039	SRR28992915	SRX24520258	SRS21267947	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Arfgef1 Hom1		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Arfgef1 Hom1\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: pools of isolated larval head	Arfgef1 Hom1	Arfgef1 Hom1	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Arfgef1_Hom1.fq.gz	fastq	3388869300.0	22592462.0	Arfgef1 Hom1.fq.gz	0:150	A:869162615;C:827706442;G:835453288;T:856534517;N:12438	150		869162615	827706442	835453288	856534517	12438	SRX24520258	SRS21267947	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32040	32040	SRR28992912	SRX24520257	SRS21267946	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Arfgef1 Het3		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Arfgef1 Het3\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: pools of isolated larval head	Arfgef1 Het3	Arfgef1 Het3	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Arfgef1_Het3.fq.gz	fastq	3369996750.0	22466645.0	Arfgef1 Het3.fq.gz	0:150	A:861941573;C:824864964;G:833793356;T:849388791;N:8066	150		861941573	824864964	833793356	849388791	8066	SRX24520257	SRS21267946	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32041	32041	SRR28992913	SRX24520256	SRS21267945	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Arfgef1 Het2		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Arfgef1 Het2\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: pools of isolated larval head	Arfgef1 Het2	Arfgef1 Het2	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Arfgef1_Het2.fq.gz	fastq	4755406500.0	31702710.0	Arfgef1 Het2.fq.gz	0:150	A:1254995507;C:1127923454;G:1138127034;T:1234180808;N:179697	150		1254995507	1127923454	1138127034	1234180808	179697	SRX24520256	SRS21267945	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32042	32042	SRR28992916	SRX24520254	SRS21267943	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Wnt8b Hom3		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Wnt8b Hom3\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: pools of isolated larval head	Wnt8b Hom3	Wnt8b Hom3	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Wnt8b_Hom3.fq.gz	fastq	5283928950.0	35226193.0	Wnt8b Hom3.fq.gz	0:150	A:1389228037;C:1262004726;G:1265392219;T:1367105548;N:198420	150		1389228037	1262004726	1265392219	1367105548	198420	SRX24520254	SRS21267943	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32043	32043	SRR28992919	SRX24520251	SRS21267940	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Wnt8b Het3		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Wnt8b Het3\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: pools of isolated larval head	Wnt8b Het3	Wnt8b Het3	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Wnt8b_Het3.fq.gz	fastq	4357330950.0	29048873.0	Wnt8b Het3.fq.gz	0:150	A:1179652667;C:1002955689;G:1008147493;T:1166494534;N:80567	150		1179652667	1002955689	1008147493	1166494534	80567	SRX24520251	SRS21267940	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
36479	36479	SRR527834	SRX171221	SRS352107	SRP014596	PRJNA171539	Transcriptomic analysis of zebrafish during development and homeostasis	GSE39703	Transcriptome Analysis	Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end 16 hpf 36 hpf 5 day larvae adult head and adult tail or paired end 24 hpf libraries Illumina. Single end reads of 36 nucleotides and paired end reads 2 x 76 nucleotides were obtained with a GAIIx Illumina. Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. Overall design: RNAseq on 5 differents samples: 24hpf embryos pool of 16 hour to 36 hour embryos 5 dpf larvea adult head and adult tail		pubmed:23684812		head	GSM977959		tissue:entire adult head\|genotype:Wild type\|strain:AB\|Stage:adult head	head	Basecalls performed using CASAVA version 1.4 Reads aligned to zebrafish genome Zv9 Ensembl with Tophat v 1.4.1 and Bowtie v 0.12.7 options: butterfly search coverage search microexon search min anchor length 5 G GTF Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file ensembl zv9 release 60 Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options u b M rRNA/Mtgenes mask G gtf Genome build: Zv9 v 60 Supplementary files format and content: .count file are the output of Htseq reads quantification. .fpkm files are the output of cufflinks quantification	entire adult head		Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions		genotype:Wild type\|strain:AB\|Stage:adult head	GSM977959	GSM977959: head; Danio rerio; RNA Seq	GSM977959 1	GSM977959: head	1		GEO Accession:GSM977959	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014596					516054600.0	14334850.0	GSM977959 r1	0:36	A:144148482;C:115800670;G:121205261;T:134746787;N:153400	36		144148482	115800670	121205261	134746787	153400	SRX171221	SRS352107	SRA056408	GEO	ITG	1	0.89668	0.12577	0.66803	0.45871	36	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2012-07-27	Adult	Adult	Head	Nervous System
39887	39887	SRR2239197	SRX1181673	SRS1053962	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant 5 hr treatment replicate 3	GSM1868446		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	mutant 5 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868446	GSM1868446: mutant 5 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868446		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868446	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_AGGCGAA.fq.gz	fastq	1486758800.0	29735176.0	GSM1868446 r1	0:50	A:407157206;C:348516474;G:333581236;T:397373823;N:130061	50		407157206	348516474	333581236	397373823	130061	SRX1181673	SRS1053962	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89356	0.24716	0.66348	0.55072	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39888	39888	SRR2239196	SRX1181672	SRS1053963	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant 5 hr treatment replicate 2	GSM1868445		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	mutant 5 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868445	GSM1868445: mutant 5 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868445		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868445	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_AATTCAT.fq.gz	fastq	1324305100.0	26486102.0	GSM1868445 r1	0:50	A:346866338;C:322967018;G:303987755;T:350367920;N:116069	50		346866338	322967018	303987755	350367920	116069	SRX1181672	SRS1053963	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.86992	0.2794	0.67087	0.45	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39889	39889	SRR2239195	SRX1181671	SRS1053965	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant 5 hr treatment replicate 1	GSM1868444		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	mutant 5 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868444	GSM1868444: mutant 5 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868444		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868444	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_CTGCAAT.fq.gz	fastq	1996223000.0	39924460.0	GSM1868444 r1	0:50	A:548376523;C:462971670;G:439194387;T:545504649;N:175771	50		548376523	462971670	439194387	545504649	175771	SRX1181671	SRS1053965	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.90072	0.27661	0.66809	0.54999	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39890	39890	SRR2239194	SRX1181670	SRS1053966	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant control replicate 3	GSM1868443		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	mutant control replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	GSM1868443	GSM1868443: mutant control replicate 3; Danio rerio; RNA Seq	GSM1868443		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868443	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_GTAAAAA.fq.gz	fastq	1689695100.0	33793902.0	GSM1868443 r1	0:50	A:469281850;C:387188418;G:368970934;T:464103273;N:150625	50		469281850	387188418	368970934	464103273	150625	SRX1181670	SRS1053966	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.88353	0.30543	0.66785	0.53952	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39891	39891	SRR2239193	SRX1181669	SRS1053964	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant control replicate 2	GSM1868442		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	mutant control replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	GSM1868442	GSM1868442: mutant control replicate 2; Danio rerio; RNA Seq	GSM1868442		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868442	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_TGGCATA.fq.gz	fastq	1744754500.0	34895090.0	GSM1868442 r1	0:50	A:475432211;C:407457752;G:387941759;T:473768506;N:154272	50		475432211	407457752	387941759	473768506	154272	SRX1181669	SRS1053964	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.8967	0.27571	0.66342	0.5413	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39892	39892	SRR2239192	SRX1181668	SRS1053967	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant control replicate 1	GSM1868441		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	mutant control replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	GSM1868441	GSM1868441: mutant control replicate 1; Danio rerio; RNA Seq	GSM1868441		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868441	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_GGAGTCC.fq.gz	fastq	1300091300.0	26001826.0	GSM1868441 r1	0:50	A:356312292;C:301731841;G:287159447;T:354773803;N:113917	50		356312292	301731841	287159447	354773803	113917	SRX1181668	SRS1053967	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89407	0.27485	0.66263	0.54402	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39893	39893	SRR2239190	SRX1181667	SRS1053968	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 3	GSM1868440		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868440	GSM1868440: wild type 5 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868440		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868440	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_GGTCCTC.fq.gz	fastq	788127550.0	15762551.0	GSM1868440 r1	0:50	A:219123307;C:174342061;G:168810140;T:225814483;N:37559	50		219123307	174342061	168810140	225814483	37559	SRX1181667	SRS1053968	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89391	0.27826	0.67034	0.55775	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39894	39894	SRR2239191	SRX1181667	SRS1053968	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 3	GSM1868440		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868440	GSM1868440: wild type 5 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868440		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868440	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_GGTCCTC.fq.gz	fastq	779058950.0	15581179.0	GSM1868440 r2	0:50	A:216843690;C:172197112;G:166801096;T:223172377;N:44675	50		216843690	172197112	166801096	223172377	44675	SRX1181667	SRS1053968	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89268	0.27974	0.67067	0.55617	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39895	39895	SRR2239188	SRX1181666	SRS1053969	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 2	GSM1868439		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868439	GSM1868439: wild type 5 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868439		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868439	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_GCTTAGA.fq.gz	fastq	884810450.0	17696209.0	GSM1868439 r1	0:50	A:244801024;C:196884736;G:189692109;T:253390454;N:42127	50		244801024	196884736	189692109	253390454	42127	SRX1181666	SRS1053969	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89625	0.26571	0.66247	0.52896	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39896	39896	SRR2239189	SRX1181666	SRS1053969	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 2	GSM1868439		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868439	GSM1868439: wild type 5 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868439		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868439	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_GCTTAGA.fq.gz	fastq	875476350.0	17509527.0	GSM1868439 r2	0:50	A:242411986;C:194719083;G:187698234;T:250595738;N:51309	50		242411986	194719083	187698234	250595738	51309	SRX1181666	SRS1053969	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89632	0.26574	0.66332	0.53633	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39897	39897	SRR2239186	SRX1181665	SRS1053970	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 1	GSM1868438		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868438	GSM1868438: wild type 5 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868438		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868438	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_GTCGATA.fq.gz	fastq	981479900.0	19629598.0	GSM1868438 r1	0:50	A:272447863;C:217586061;G:210457740;T:280941539;N:46697	50		272447863	217586061	210457740	280941539	46697	SRX1181665	SRS1053970	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89259	0.28519	0.66413	0.54434	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39898	39898	SRR2239187	SRX1181665	SRS1053970	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 1	GSM1868438		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868438	GSM1868438: wild type 5 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868438		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868438	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_GTCGATA.fq.gz	fastq	970627300.0	19412546.0	GSM1868438 r2	0:50	A:269587370;C:215107358;G:208077535;T:277799059;N:55978	50		269587370	215107358	208077535	277799059	55978	SRX1181665	SRS1053970	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.8924	0.2863	0.66486	0.54277	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39899	39899	SRR2239184	SRX1181664	SRS1053971	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 3	GSM1868437		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868437	GSM1868437: wild type 2 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868437		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868437	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_AGATACT.fq.gz	fastq	1034107450.0	20682149.0	GSM1868437 r1	0:50	A:263807622;C:250451504;G:242163638;T:277636652;N:48034	50		263807622	250451504	242163638	277636652	48034	SRX1181664	SRS1053971	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.90878	0.23218	0.65916	0.49411	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39900	39900	SRR2239185	SRX1181664	SRS1053971	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 3	GSM1868437		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868437	GSM1868437: wild type 2 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868437		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868437	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_AGATACT.fq.gz	fastq	1021705150.0	20434103.0	GSM1868437 r2	0:50	A:260838269;C:247381617;G:239188036;T:274238961;N:58267	50		260838269	247381617	239188036	274238961	58267	SRX1181664	SRS1053971	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.91116	0.23255	0.65918	0.49596	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39901	39901	SRR2239182	SRX1181663	SRS1053972	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 2	GSM1868436		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868436	GSM1868436: wild type 2 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868436		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868436	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_GGGTCAA.fq.gz	fastq	756008650.0	15120173.0	GSM1868436 r1	0:50	A:209261412;C:168123618;G:163450516;T:215134424;N:38680	50		209261412	168123618	163450516	215134424	38680	SRX1181663	SRS1053972	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.8978	0.26699	0.66172	0.53653	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39902	39902	SRR2239183	SRX1181663	SRS1053972	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 2	GSM1868436		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868436	GSM1868436: wild type 2 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868436		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868436	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_GGGTCAA.fq.gz	fastq	747959000.0	14959180.0	GSM1868436 r2	0:50	A:207110574;C:166254650;G:161670187;T:212878047;N:45542	50		207110574	166254650	161670187	212878047	45542	SRX1181663	SRS1053972	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89508	0.26657	0.66373	0.53734	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39903	39903	SRR2239180	SRX1181662	SRS1053973	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 1	GSM1868435		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868435	GSM1868435: wild type 2 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868435		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868435	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_CAATATC.fq.gz	fastq	843938700.0	16878774.0	GSM1868435 r1	0:50	A:235353785;C:185755129;G:180220044;T:242567413;N:42329	50		235353785	185755129	180220044	242567413	42329	SRX1181662	SRS1053973	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.8819	0.31587	0.6719	0.53852	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39904	39904	SRR2239181	SRX1181662	SRS1053973	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 1	GSM1868435		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868435	GSM1868435: wild type 2 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868435		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868435	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_CAATATC.fq.gz	fastq	837375500.0	16747510.0	GSM1868435 r2	0:50	A:233691274;C:184249473;G:178762050;T:240622009;N:50694	50		233691274	184249473	178762050	240622009	50694	SRX1181662	SRS1053973	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.88228	0.31306	0.67042	0.53933	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39905	39905	SRR2239178	SRX1181661	SRS1053976	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 3	GSM1868434		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868434	GSM1868434: wild type control replicate 3; Danio rerio; RNA Seq	GSM1868434		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868434	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_ACCCACT.fq.gz	fastq	946427500.0	18928550.0	GSM1868434 r1	0:50	A:260851494;C:211313068;G:205344403;T:268874280;N:44255	50		260851494	211313068	205344403	268874280	44255	SRX1181661	SRS1053976	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89626	0.27082	0.66058	0.53343	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39906	39906	SRR2239179	SRX1181661	SRS1053976	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 3	GSM1868434		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868434	GSM1868434: wild type control replicate 3; Danio rerio; RNA Seq	GSM1868434		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868434	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_ACCCACT.fq.gz	fastq	935318450.0	18706369.0	GSM1868434 r2	0:50	A:258004973;C:208706255;G:202911059;T:265642847;N:53316	50		258004973	208706255	202911059	265642847	53316	SRX1181661	SRS1053976	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89576	0.27216	0.663	0.53587	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39907	39907	SRR2239176	SRX1181660	SRS1053974	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 2	GSM1868433		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868433	GSM1868433: wild type control replicate 2; Danio rerio; RNA Seq	GSM1868433		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868433	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_TCAACTG.fq.gz	fastq	914021500.0	18280430.0	GSM1868433 r1	0:50	A:252009242;C:204125475;G:197760562;T:260083313;N:42908	50		252009242	204125475	197760562	260083313	42908	SRX1181660	SRS1053974	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89646	0.26998	0.65979	0.53202	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39908	39908	SRR2239177	SRX1181660	SRS1053974	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 2	GSM1868433		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868433	GSM1868433: wild type control replicate 2; Danio rerio; RNA Seq	GSM1868433		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868433	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_TCAACTG.fq.gz	fastq	904836300.0	18096726.0	GSM1868433 r2	0:50	A:249726925;C:201939252;G:195727802;T:257389594;N:52727	50		249726925	201939252	195727802	257389594	52727	SRX1181660	SRS1053974	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89504	0.27105	0.6607	0.5314	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39909	39909	SRR2239174	SRX1181659	SRS1053975	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 1	GSM1868432		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868432	GSM1868432: wild type control replicate 1; Danio rerio; RNA Seq	GSM1868432		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868432	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_TTTAACT.fq.gz	fastq	919147800.0	18382956.0	GSM1868432 r1	0:50	A:255238211;C:203629686;G:197780664;T:262454873;N:44366	50		255238211	203629686	197780664	262454873	44366	SRX1181659	SRS1053975	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89498	0.2793	0.6636	0.54563	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39910	39910	SRR2239175	SRX1181659	SRS1053975	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 1	GSM1868432		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.		age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868432	GSM1868432: wild type control replicate 1; Danio rerio; RNA Seq	GSM1868432		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868432	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_TTTAACT.fq.gz	fastq	908786950.0	18175739.0	GSM1868432 r2	0:50	A:252518589;C:201251252;G:195514386;T:259449857;N:52866	50		252518589	201251252	195514386	259449857	52866	SRX1181659	SRS1053975	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89351	0.27857	0.66492	0.54418	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
41655	41655	SRR5115728	SRX2431099	SRS1866976	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep5	GSM2430667		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep5	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430667	GSM2430667: 18 hpi rep5; Danio rerio; RNA Seq	GSM2430667		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430667	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_54366.fastq.gz	fastq	3043532908.0	58529479.0	GSM2430667 r1	0:52	A:729034781;C:769509924;G:743085356;T:801831768;N:71079	52		729034781	769509924	743085356	801831768	71079	SRX2431099	SRS1866976	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.73906	0.22225	0.74061	0.49988	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41656	41656	SRR5115727	SRX2431098	SRS1866975	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep4	GSM2430666		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep4	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430666	GSM2430666: 18 hpi rep4; Danio rerio; RNA Seq	GSM2430666		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430666	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_48592.fastq.gz	fastq	2622132240.0	50425620.0	GSM2430666 r1	0:52	A:566371236;C:777180578;G:659521124;T:618999154;N:60148	52		566371236	777180578	659521124	618999154	60148	SRX2431098	SRS1866975	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.92057	0.28475	0.86833	0.72823	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41657	41657	SRR5115726	SRX2431097	SRS1866974	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep3	GSM2430665		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep3	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430665	GSM2430665: 18 hpi rep3; Danio rerio; RNA Seq	GSM2430665		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430665	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_48591.fastq.gz	fastq	2478119176.0	47656138.0	GSM2430665 r1	0:52	A:493736890;C:768557459;G:661870968;T:553896608;N:57251	52		493736890	768557459	661870968	553896608	57251	SRX2431097	SRS1866974	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.96537	0.26164	0.87892	0.7204	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41658	41658	SRR5115725	SRX2431096	SRS1866973	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep2	GSM2430664		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep2	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430664	GSM2430664: 18 hpi rep2; Danio rerio; RNA Seq	GSM2430664		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430664	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_48590.fastq.gz	fastq	2414695452.0	46436451.0	GSM2430664 r1	0:52	A:475090050;C:755838280;G:657771658;T:525939134;N:56330	52		475090050	755838280	657771658	525939134	56330	SRX2431096	SRS1866973	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.9654	0.26982	0.89676	0.72161	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41659	41659	SRR5115724	SRX2431095	SRS1866972	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep1	GSM2430663		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep1	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430663	GSM2430663: 18 hpi rep1; Danio rerio; RNA Seq	GSM2430663		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430663	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_48589.fastq.gz	fastq	2275983060.0	43768905.0	GSM2430663 r1	0:52	A:466133336;C:694614756;G:598071579;T:517110546;N:52843	52		466133336	694614756	598071579	517110546	52843	SRX2431095	SRS1866972	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.94909	0.2695	0.86809	0.70019	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41660	41660	SRR5115723	SRX2431094	SRS1866971	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep5	GSM2430662		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep5	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430662	GSM2430662: 9 hpi rep5; Danio rerio; RNA Seq	GSM2430662		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430662	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_54368.fastq.gz	fastq	2831111348.0	54444449.0	GSM2430662 r1	0:52	A:674270099;C:713818041;G:694997603;T:747958840;N:66765	52		674270099	713818041	694997603	747958840	66765	SRX2431094	SRS1866971	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.81449	0.24117	0.74091	0.53961	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41661	41661	SRR5115722	SRX2431093	SRS1866970	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep4	GSM2430661		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep4	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430661	GSM2430661: 9 hpi rep4; Danio rerio; RNA Seq	GSM2430661		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430661	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_48586.fastq.gz	fastq	3247890880.0	62459440.0	GSM2430661 r1	0:52	A:737775958;C:866361850;G:806031275;T:837644754;N:77043	52		737775958	866361850	806031275	837644754	77043	SRX2431093	SRS1866970	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.88824	0.26531	0.77619	0.64707	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41662	41662	SRR5115721	SRX2431092	SRS1866969	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep3	GSM2430660		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep3	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430660	GSM2430660: 9 hpi rep3; Danio rerio; RNA Seq	GSM2430660		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430660	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_48585.fastq.gz	fastq	2383588948.0	45838249.0	GSM2430660 r1	0:52	A:471509922;C:736118462;G:639172021;T:536732824;N:55719	52		471509922	736118462	639172021	536732824	55719	SRX2431092	SRS1866969	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.96831	0.25406	0.88327	0.69186	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41663	41663	SRR5115720	SRX2431091	SRS1866968	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep2	GSM2430659		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep2	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430659	GSM2430659: 9 hpi rep2; Danio rerio; RNA Seq	GSM2430659		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430659	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_48584.fastq.gz	fastq	2858494184.0	54971042.0	GSM2430659 r1	0:52	A:601123087;C:841668883;G:744364922;T:671270980;N:66312	52		601123087	841668883	744364922	671270980	66312	SRX2431091	SRS1866968	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.93531	0.28407	0.86277	0.73297	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41664	41664	SRR5115719	SRX2431090	SRS1866967	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep1	GSM2430658		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep1	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430658	GSM2430658: 9 hpi rep1; Danio rerio; RNA Seq	GSM2430658		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430658	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_48583.fastq.gz	fastq	2348023808.0	45154304.0	GSM2430658 r1	0:52	A:520788777;C:655035758;G:589264364;T:582879912;N:54997	52		520788777	655035758	589264364	582879912	54997	SRX2431090	SRS1866967	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.90637	0.26958	0.80649	0.68165	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41665	41665	SRR5115718	SRX2431089	SRS1866966	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		0 hpi rep4	GSM2430657		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	0 hpi rep4	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	GSM2430657	GSM2430657: 0 hpi rep4; Danio rerio; RNA Seq	GSM2430657		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430657	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			0hpi_54367.fastq.gz	fastq	3737365060.0	71872405.0	GSM2430657 r1	0:52	A:898855616;C:929504130;G:883445728;T:1025471492;N:88094	52		898855616	929504130	883445728	1025471492	88094	SRX2431089	SRS1866966	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.80824	0.21971	0.75511	0.45635	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41666	41666	SRR5115717	SRX2431088	SRS1866965	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		0 hpi rep3	GSM2430656		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	0 hpi rep3	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	GSM2430656	GSM2430656: 0 hpi rep3; Danio rerio; RNA Seq	GSM2430656		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430656	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			0hpi_54365.fastq.gz	fastq	2479423440.0	47681220.0	GSM2430656 r1	0:52	A:585035619;C:641794408;G:600148220;T:652388942;N:56251	52		585035619	641794408	600148220	652388942	56251	SRX2431088	SRS1866965	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.7459	0.20704	0.76674	0.44617	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41667	41667	SRR5115716	SRX2431087	SRS1866964	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		0 hpi rep2	GSM2430655		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	0 hpi rep2	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	GSM2430655	GSM2430655: 0 hpi rep2; Danio rerio; RNA Seq	GSM2430655		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430655	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			0hpi_48587.fastq.gz	fastq	2251744196.0	43302773.0	GSM2430655 r1	0:52	A:446930339;C:692500195;G:602614693;T:509646110;N:52859	52		446930339	692500195	602614693	509646110	52859	SRX2431087	SRS1866964	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.96295	0.25309	0.90035	0.717	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41668	41668	SRR5115715	SRX2431086	SRS1866963	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		0 hpi rep1	GSM2430654		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	0 hpi rep1	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	GSM2430654	GSM2430654: 0 hpi rep1; Danio rerio; RNA Seq	GSM2430654		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430654	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			0hpi_44113.fastq.gz	fastq	2656056728.0	51078014.0	GSM2430654 r1	0:52	A:652742098;C:649243306;G:612049135;T:741907471;N:114718	52		652742098	649243306	612049135	741907471	114718	SRX2431086	SRS1866963	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.85198	0.24059	0.73357	0.48804	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
48776	48776	SRR7299203	SRX4201637	SRS3411871	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT3b	GSM3188319		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT3b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188319	GSM3188319: WT3b; Danio rerio; RNA Seq	GSM3188319		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188319	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			4_WT_GTGAAA_L002_R1_001.fastq.gz	fastq	1515830415.0	29722165.0	GSM3188319 r1	0:51 1:0	A:394794389;C:366496372;G:355480667;T:399049574;N:9413	51	0	394794389	366496372	355480667	399049574	9413	SRX4201637	SRS3411871	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91648	0.0991	0.66042	0.46623	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48777	48777	SRR7299202	SRX4201636	SRS3411870	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT3a	GSM3188318		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT3a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188318	GSM3188318: WT3a; Danio rerio; RNA Seq	GSM3188318		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188318	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			4_WT_GTGAAA_L001_R1_001.fastq.gz	fastq	1530012342.0	30000242.0	GSM3188318 r1	0:51 1:0	A:398681114;C:369811969;G:358638504;T:402843884;N:36871	51	0	398681114	369811969	358638504	402843884	36871	SRX4201636	SRS3411870	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91534	0.09956	0.65827	0.46141	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48778	48778	SRR7299201	SRX4201635	SRS3411869	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT2b	GSM3188317		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT2b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188317	GSM3188317: WT2b; Danio rerio; RNA Seq	GSM3188317		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188317	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			3_WT_CAGATC_L002_R1_001.fastq.gz	fastq	1369591128.0	26854728.0	GSM3188317 r1	0:51 1:0	A:357550847;C:329596101;G:321156412;T:361279585;N:8183	51	0	357550847	329596101	321156412	361279585	8183	SRX4201635	SRS3411869	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91614	0.1006	0.66103	0.45858	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48779	48779	SRR7299200	SRX4201634	SRS3411868	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT2a	GSM3188316		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT2a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188316	GSM3188316: WT2a; Danio rerio; RNA Seq	GSM3188316		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188316	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			3_WT_CAGATC_L001_R1_001.fastq.gz	fastq	1382657328.0	27110928.0	GSM3188316 r1	0:51 1:0	A:361162409;C:332612483;G:324077790;T:364769956;N:34690	51	0	361162409	332612483	324077790	364769956	34690	SRX4201634	SRS3411868	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91539	0.10075	0.65817	0.4455	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48780	48780	SRR7299199	SRX4201633	SRS3411867	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT1b	GSM3188315		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT1b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188315	GSM3188315: WT1b; Danio rerio; RNA Seq	GSM3188315		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188315	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			1_WT_ACAGTG_L002_R1_001.fastq.gz	fastq	1524014640.0	29882640.0	GSM3188315 r1	0:51 1:0	A:396270551;C:368829474;G:359483222;T:399422211;N:9182	51	0	396270551	368829474	359483222	399422211	9182	SRX4201633	SRS3411867	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91922	0.09077	0.65447	0.45526	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48781	48781	SRR7299198	SRX4201632	SRS3411866	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT1a	GSM3188314		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT1a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188314	GSM3188314: WT1a; Danio rerio; RNA Seq	GSM3188314		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188314	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			1_WT_ACAGTG_L001_R1_001.fastq.gz	fastq	1538497671.0	30166621.0	GSM3188314 r1	0:51 1:0	A:400221457;C:372214397;G:362764636;T:403260458;N:36723	51	0	400221457	372214397	362764636	403260458	36723	SRX4201632	SRS3411866	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91885	0.09093	0.65529	0.45611	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48782	48782	SRR7299197	SRX4201631	SRS3411865	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut3b	GSM3188313		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut3b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188313	GSM3188313: Mut3b; Danio rerio; RNA Seq	GSM3188313		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188313	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			4_HOM_CTTGTA_L002_R1_001.fastq.gz	fastq	1461642252.0	28659652.0	GSM3188313 r1	0:51 1:0	A:378302770;C:355129502;G:346531981;T:381669069;N:8930	51	0	378302770	355129502	346531981	381669069	8930	SRX4201631	SRS3411865	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.92266	0.08429	0.65376	0.47318	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48783	48783	SRR7299196	SRX4201630	SRS3411864	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut3a	GSM3188312		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut3a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188312	GSM3188312: Mut3a; Danio rerio; RNA Seq	GSM3188312		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188312	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			4_HOM_CTTGTA_L001_R1_001.fastq.gz	fastq	1475994978.0	28941078.0	GSM3188312 r1	0:51 1:0	A:382182767;C:358528625;G:349827681;T:385419945;N:35960	51	0	382182767	358528625	349827681	385419945	35960	SRX4201630	SRS3411864	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.92088	0.0857	0.65525	0.47511	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48784	48784	SRR7299195	SRX4201629	SRS3411863	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut2b	GSM3188311		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut2b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188311	GSM3188311: Mut2b; Danio rerio; RNA Seq	GSM3188311		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188311	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			3_HOM_GCCAAT_L002_R1_001.fastq.gz	fastq	1590786798.0	31191898.0	GSM3188311 r1	0:51 1:0	A:415295793;C:382664391;G:373902522;T:418914651;N:9441	51	0	415295793	382664391	373902522	418914651	9441	SRX4201629	SRS3411863	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91457	0.10759	0.65675	0.45366	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48785	48785	SRR7299194	SRX4201628	SRS3411862	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut2a	GSM3188310		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut2a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188310	GSM3188310: Mut2a; Danio rerio; RNA Seq	GSM3188310		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188310	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			3_HOM_GCCAAT_L001_R1_001.fastq.gz	fastq	1605491628.0	31480228.0	GSM3188310 r1	0:51 1:0	A:419379536;C:386061723;G:377175409;T:422836209;N:38751	51	0	419379536	386061723	377175409	422836209	38751	SRX4201628	SRS3411862	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91489	0.10727	0.65695	0.45692	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48786	48786	SRR7299193	SRX4201627	SRS3411861	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut1b	GSM3188309		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut1b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188309	GSM3188309: Mut1b; Danio rerio; RNA Seq	GSM3188309		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188309	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			1_HOM_CGATGT_L002_R1_001.fastq.gz	fastq	1573374939.0	30850489.0	GSM3188309 r1	0:51 1:0	A:410076423;C:380158239;G:370121507;T:413009312;N:9458	51	0	410076423	380158239	370121507	413009312	9458	SRX4201627	SRS3411861	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91645	0.09702	0.65366	0.4502	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48787	48787	SRR7299192	SRX4201626	SRS3411860	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut1a	GSM3188308		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut1a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.		strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188308	GSM3188308: Mut1a; Danio rerio; RNA Seq	GSM3188308		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188308	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			1_HOM_CGATGT_L001_R1_001.fastq.gz	fastq	1587939009.0	31136059.0	GSM3188308 r1	0:51 1:0	A:414049125;C:383523892;G:373426588;T:416900791;N:38613	51	0	414049125	383523892	373426588	416900791	38613	SRX4201626	SRS3411860	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
50664	50664	SRR8244112	SRX5062217	SRS4078157	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep5	GSM3488843		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep5	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488843	GSM3488843: ncapg2 gRNA3 Cas9 rep5; Danio rerio; RNA Seq	GSM3488843		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488843	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S15_S15_L001_R1_001.fastq.gz	fastq	1104353541.0	21653991.0	GSM3488843 r1	0:51 1:0	A:271859663;C:271742909;G:255256859;T:305383003;N:111107	51	0	271859663	271742909	255256859	305383003	111107	SRX5062217	SRS4078157	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92793	0.15706	0.6686	0.48785	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50665	50665	SRR8244113	SRX5062217	SRS4078157	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep5	GSM3488843		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep5	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488843	GSM3488843: ncapg2 gRNA3 Cas9 rep5; Danio rerio; RNA Seq	GSM3488843		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488843	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S15_S15_L002_R1_001.fastq.gz	fastq	1107061335.0	21707085.0	GSM3488843 r2	0:51 1:0	A:272582305;C:272363181;G:255837702;T:306158767;N:119380	51	0	272582305	272363181	255837702	306158767	119380	SRX5062217	SRS4078157	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.9291	0.15688	0.66939	0.4874	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50666	50666	SRR8244114	SRX5062217	SRS4078157	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep5	GSM3488843		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep5	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488843	GSM3488843: ncapg2 gRNA3 Cas9 rep5; Danio rerio; RNA Seq	GSM3488843		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488843	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S15_S15_L003_R1_001.fastq.gz	fastq	1108045737.0	21726387.0	GSM3488843 r3	0:51 1:0	A:272751963;C:272598901;G:256278919;T:306301107;N:114847	51	0	272751963	272598901	256278919	306301107	114847	SRX5062217	SRS4078157	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92569	0.15636	0.67107	0.48848	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50667	50667	SRR8244109	SRX5062216	SRS4078156	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep4	GSM3488842		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep4	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488842	GSM3488842: ncapg2 gRNA3 Cas9 rep4; Danio rerio; RNA Seq	GSM3488842		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488842	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S14_S14_L001_R1_001.fastq.gz	fastq	1006920234.0	19743534.0	GSM3488842 r1	0:51 1:0	A:250914585;C:242617209;G:230819870;T:282467195;N:101375	51	0	250914585	242617209	230819870	282467195	101375	SRX5062216	SRS4078156	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92511	0.14656	0.66255	0.4737	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50668	50668	SRR8244110	SRX5062216	SRS4078156	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep4	GSM3488842		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep4	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488842	GSM3488842: ncapg2 gRNA3 Cas9 rep4; Danio rerio; RNA Seq	GSM3488842		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488842	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S14_S14_L002_R1_001.fastq.gz	fastq	1011359019.0	19830569.0	GSM3488842 r2	0:51 1:0	A:252043979;C:243615191;G:231854021;T:283736741;N:109087	51	0	252043979	243615191	231854021	283736741	109087	SRX5062216	SRS4078156	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92626	0.14636	0.66113	0.47444	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50669	50669	SRR8244111	SRX5062216	SRS4078156	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep4	GSM3488842		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep4	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488842	GSM3488842: ncapg2 gRNA3 Cas9 rep4; Danio rerio; RNA Seq	GSM3488842		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488842	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S14_S14_L003_R1_001.fastq.gz	fastq	1013403201.0	19870651.0	GSM3488842 r3	0:51 1:0	A:252575184;C:244090867;G:232476280;T:284156056;N:104814	51	0	252575184	244090867	232476280	284156056	104814	SRX5062216	SRS4078156	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92435	0.14732	0.66178	0.47364	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50670	50670	SRR8244106	SRX5062215	SRS4078155	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep3	GSM3488841		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep3	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488841	GSM3488841: ncapg2 gRNA3 Cas9 rep3; Danio rerio; RNA Seq	GSM3488841		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488841	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S13_S13_L001_R1_001.fastq.gz	fastq	994771983.0	19505333.0	GSM3488841 r1	0:51 1:0	A:242678169;C:243280763;G:232480047;T:276234852;N:98152	51	0	242678169	243280763	232480047	276234852	98152	SRX5062215	SRS4078155	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.93015	0.13516	0.66338	0.47268	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50671	50671	SRR8244107	SRX5062215	SRS4078155	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep3	GSM3488841		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep3	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488841	GSM3488841: ncapg2 gRNA3 Cas9 rep3; Danio rerio; RNA Seq	GSM3488841		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488841	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S13_S13_L002_R1_001.fastq.gz	fastq	1000961139.0	19626689.0	GSM3488841 r2	0:51 1:0	A:244193037;C:244754957;G:233915568;T:277991308;N:106269	51	0	244193037	244754957	233915568	277991308	106269	SRX5062215	SRS4078155	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92992	0.13363	0.66143	0.47596	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50672	50672	SRR8244108	SRX5062215	SRS4078155	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep3	GSM3488841		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep3	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488841	GSM3488841: ncapg2 gRNA3 Cas9 rep3; Danio rerio; RNA Seq	GSM3488841		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488841	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S13_S13_L003_R1_001.fastq.gz	fastq	1002999507.0	19666657.0	GSM3488841 r3	0:51 1:0	A:244687169;C:245305809;G:234523016;T:278381509;N:102004	51	0	244687169	245305809	234523016	278381509	102004	SRX5062215	SRS4078155	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92775	0.13351	0.66143	0.46661	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50673	50673	SRR8244103	SRX5062214	SRS4078154	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep2	GSM3488840		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep2	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488840	GSM3488840: ncapg2 gRNA3 Cas9 rep2; Danio rerio; RNA Seq	GSM3488840		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488840	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S12_S12_L001_R1_001.fastq.gz	fastq	1228909821.0	24096271.0	GSM3488840 r1	0:51 1:0	A:298212594;C:304802527;G:286549620;T:339221142;N:123938	51	0	298212594	304802527	286549620	339221142	123938	SRX5062214	SRS4078154	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92713	0.14665	0.66547	0.49543	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50674	50674	SRR8244104	SRX5062214	SRS4078154	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep2	GSM3488840		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep2	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488840	GSM3488840: ncapg2 gRNA3 Cas9 rep2; Danio rerio; RNA Seq	GSM3488840		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488840	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S12_S12_L002_R1_001.fastq.gz	fastq	1235947821.0	24234271.0	GSM3488840 r2	0:51 1:0	A:299963399;C:306522449;G:288138725;T:341187728;N:135520	51	0	299963399	306522449	288138725	341187728	135520	SRX5062214	SRS4078154	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92688	0.14676	0.66669	0.49493	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50675	50675	SRR8244105	SRX5062214	SRS4078154	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep2	GSM3488840		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep2	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488840	GSM3488840: ncapg2 gRNA3 Cas9 rep2; Danio rerio; RNA Seq	GSM3488840		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488840	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S12_S12_L003_R1_001.fastq.gz	fastq	1236009531.0	24235481.0	GSM3488840 r3	0:51 1:0	A:300016555;C:306493432;G:288334228;T:341035993;N:129323	51	0	300016555	306493432	288334228	341035993	129323	SRX5062214	SRS4078154	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92486	0.1456	0.66576	0.49558	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50676	50676	SRR8244100	SRX5062213	SRS4078153	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep1	GSM3488839		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep1	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488839	GSM3488839: ncapg2 gRNA3 Cas9 rep1; Danio rerio; RNA Seq	GSM3488839		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488839	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S11_S11_L001_R1_001.fastq.gz	fastq	1090927536.0	21390736.0	GSM3488839 r1	0:51 1:0	A:271017299;C:263543757;G:249256774;T:306999426;N:110280	51	0	271017299	263543757	249256774	306999426	110280	SRX5062213	SRS4078153	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92359	0.15259	0.65662	0.47976	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50677	50677	SRR8244101	SRX5062213	SRS4078153	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep1	GSM3488839		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep1	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488839	GSM3488839: ncapg2 gRNA3 Cas9 rep1; Danio rerio; RNA Seq	GSM3488839		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488839	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S11_S11_L002_R1_001.fastq.gz	fastq	1096424775.0	21498525.0	GSM3488839 r2	0:51 1:0	A:272497776;C:264812949;G:250461572;T:308534070;N:118408	51	0	272497776	264812949	250461572	308534070	118408	SRX5062213	SRS4078153	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92537	0.15294	0.6564	0.48091	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50678	50678	SRR8244102	SRX5062213	SRS4078153	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 Cas9 rep1	GSM3488839		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 Cas9 rep1	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488839	GSM3488839: ncapg2 gRNA3 Cas9 rep1; Danio rerio; RNA Seq	GSM3488839		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488839	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S11_S11_L003_R1_001.fastq.gz	fastq	1097236746.0	21514446.0	GSM3488839 r3	0:51 1:0	A:272640711;C:265014569;G:250849083;T:308618948;N:113435	51	0	272640711	265014569	250849083	308618948	113435	SRX5062213	SRS4078153	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92126	0.15288	0.65758	0.48139	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50679	50679	SRR8244097	SRX5062212	SRS4078152	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep5	GSM3488838		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep5	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488838	GSM3488838: ncapg2 gRNA3 rep5; Danio rerio; RNA Seq	GSM3488838		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488838	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S10_S10_L001_R1_001.fastq.gz	fastq	1108278552.0	21730952.0	GSM3488838 r1	0:51 1:0	A:275932434;C:266759397;G:253066873;T:312409285;N:110563	51	0	275932434	266759397	253066873	312409285	110563	SRX5062212	SRS4078152	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92384	0.15395	0.65981	0.47171	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50680	50680	SRR8244098	SRX5062212	SRS4078152	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep5	GSM3488838		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep5	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488838	GSM3488838: ncapg2 gRNA3 rep5; Danio rerio; RNA Seq	GSM3488838		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488838	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S10_S10_L002_R1_001.fastq.gz	fastq	1112805975.0	21819725.0	GSM3488838 r2	0:51 1:0	A:277089394;C:267821306;G:254016353;T:313757990;N:120932	51	0	277089394	267821306	254016353	313757990	120932	SRX5062212	SRS4078152	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92569	0.15411	0.66042	0.47795	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50681	50681	SRR8244099	SRX5062212	SRS4078152	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep5	GSM3488838		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep5	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488838	GSM3488838: ncapg2 gRNA3 rep5; Danio rerio; RNA Seq	GSM3488838		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488838	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S10_S10_L003_R1_001.fastq.gz	fastq	1113574698.0	21834798.0	GSM3488838 r3	0:51 1:0	A:277244311;C:268029085;G:254374324;T:313812352;N:114626	51	0	277244311	268029085	254374324	313812352	114626	SRX5062212	SRS4078152	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92312	0.15403	0.66131	0.475	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50682	50682	SRR8244094	SRX5062211	SRS4078151	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep4	GSM3488837		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep4	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488837	GSM3488837: ncapg2 gRNA3 rep4; Danio rerio; RNA Seq	GSM3488837		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488837	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S9_S9_L001_R1_001.fastq.gz	fastq	989308914.0	19398214.0	GSM3488837 r1	0:51 1:0	A:244142324;C:238841091;G:227525215;T:278701440;N:98844	51	0	244142324	238841091	227525215	278701440	98844	SRX5062211	SRS4078151	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92369	0.14203	0.66107	0.47606	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50683	50683	SRR8244095	SRX5062211	SRS4078151	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep4	GSM3488837		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep4	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488837	GSM3488837: ncapg2 gRNA3 rep4; Danio rerio; RNA Seq	GSM3488837		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488837	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S9_S9_L002_R1_001.fastq.gz	fastq	995567991.0	19520941.0	GSM3488837 r2	0:51 1:0	A:245733399;C:240305756;G:228973873;T:280447377;N:107586	51	0	245733399	240305756	228973873	280447377	107586	SRX5062211	SRS4078151	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.9253	0.14267	0.66156	0.47641	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50684	50684	SRR8244096	SRX5062211	SRS4078151	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep4	GSM3488837		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep4	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488837	GSM3488837: ncapg2 gRNA3 rep4; Danio rerio; RNA Seq	GSM3488837		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488837	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S9_S9_L003_R1_001.fastq.gz	fastq	995686107.0	19523257.0	GSM3488837 r3	0:51 1:0	A:245728339;C:240375764;G:229145692;T:280334702;N:101610	51	0	245728339	240375764	229145692	280334702	101610	SRX5062211	SRS4078151	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.9222	0.1414	0.66129	0.47546	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50685	50685	SRR8244091	SRX5062210	SRS4078150	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep3	GSM3488836		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep3	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488836	GSM3488836: ncapg2 gRNA3 rep3; Danio rerio; RNA Seq	GSM3488836		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488836	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S8_S8_L001_R1_001.fastq.gz	fastq	1240305720.0	24319720.0	GSM3488836 r1	0:51 1:0	A:306283941;C:302350915;G:285978262;T:345570234;N:122368	51	0	306283941	302350915	285978262	345570234	122368	SRX5062210	SRS4078150	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92431	0.15332	0.6664	0.48826	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50686	50686	SRR8244092	SRX5062210	SRS4078150	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep3	GSM3488836		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep3	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488836	GSM3488836: ncapg2 gRNA3 rep3; Danio rerio; RNA Seq	GSM3488836		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488836	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S8_S8_L002_R1_001.fastq.gz	fastq	1244343033.0	24398883.0	GSM3488836 r2	0:51 1:0	A:307334069;C:303294657;G:286891055;T:346690285;N:132967	51	0	307334069	303294657	286891055	346690285	132967	SRX5062210	SRS4078150	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92593	0.15367	0.66604	0.4866	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50687	50687	SRR8244093	SRX5062210	SRS4078150	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep3	GSM3488836		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep3	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488836	GSM3488836: ncapg2 gRNA3 rep3; Danio rerio; RNA Seq	GSM3488836		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488836	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S8_S8_L003_R1_001.fastq.gz	fastq	1246263744.0	24436544.0	GSM3488836 r3	0:51 1:0	A:307763481;C:303768183;G:287566818;T:347039016;N:126246	51	0	307763481	303768183	287566818	347039016	126246	SRX5062210	SRS4078150	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92279	0.15465	0.6662	0.48909	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System
50688	50688	SRR8244088	SRX5062209	SRS4078149	SRP170713	PRJNA506958	Mutations in NCAPG2 cause a severe neurodevelopmental syndrome that expands the phenotypic spectrum of condensinopathies	GSE122932	Transcriptome Analysis	The use of whole exome/genome sequencing has been a catalyst for a genotype first approach to diagnostics. Under this paradigm we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2 we found abnormal chromosome condensation augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1 a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype we co suppressed nphp1 and ncapg2 which resulted in significantly more dysplastic renal tubules. Together our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus. Overall design: To investigate the global impact of NCAPG2 loss in an in vivo developmental context we performed transcriptome profiling of zebrafish embryo heads isolated at 2 dpf injected with gRNA1 alone or gRNA1+Cas9; 5 biological replicates		pubmed:30609410		ncapg2 gRNA3 rep2	GSM3488835		source name:embryo head\|tissue:embryo head\|time point:2 dpf	ncapg2 gRNA3 rep2	Data were demultiplexed and Fastq files generated using Bcl2Fastq Illumina. RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt post trimming were kept. Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA seq alignment tool. Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis. Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment. Genome build: Zv10r87 Supplementary files format and content: Excel file include RPKM values for each Sample	embryo head		We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer’s protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	Embryos were obtained from natural matings of adult wild type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media 0.3 g/L NaCl 75 mg/L CaSO4 37.5 mg/L NaHC03 0.003% methylene blue at 28°C until 2 dpf.	tissue:embryo head\|time point:2 dpf	GSM3488835	GSM3488835: ncapg2 gRNA3 rep2; Danio rerio; RNA Seq	GSM3488835		1	We extracted total RNA from embryo heads with Trizol ThermoFisher according to manufacturer's instructions. N=20 embryos/pool RNAseq libraries were prepared using the Stranded mRNA Seq Kit KAPA following the manufacturer's protocol. In brief mRNA transcripts were captured using magnetic oligo dT beads fragmented with heat and magnesium and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. All libraries were pooled in equimolar ratio 5 libraries/lane and sequenced on an Illumina HiSeq 4000 flow cell to yield 66 million 50 bp single end sequences per sample.	GEO Accession:GSM3488835	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP170713			4948-S7_S7_L001_R1_001.fastq.gz	fastq	1047071514.0	20530814.0	GSM3488835 r1	0:51 1:0	A:256902869;C:258344237;G:242502701;T:289217725;N:103982	51	0	256902869	258344237	242502701	289217725	103982	SRX5062209	SRS4078149	SRA814826	GEO	Center for Human Disease Modeling, Duke University Medical Center	1	0.92959	0.1635	0.66647	0.49696	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-11-26	Hatching	Embryo	Head	Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;