metadata: run_metadata: 150 rows where experiment.library_layout = "SINGLE", experiment.platform = "ILLUMINA" and tissue_curation

150 rows where experiment.library_layout = "SINGLE", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Renal System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.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
38296	38296	SRR1647681	SRX756916	SRS742120	SRP049663	PRJNA266803	Spring Varaemia of Carp Virus SVCV infection of adult zebrafish	GSE63133	Transcriptome Analysis	During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.		pubmed:25535281	24K	GSM1541905	source name:head kidney\|tissue:head kidney\|disease state:24h post SVCV infection	24K	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	head kidney		Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:head kidney\|disease state:24h post SVCV infection	GSM1541905	GSM1541905: 24K; Danio rerio; RNA Seq	GSM1541905		1	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1541905	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP049663		24K_GTGAAA_L003_R1.fastq	fastq	1020487560.0	20009560.0	GSM1541905 r1	0:51	A:266117014;C:246797067;G:240014464;T:267491299;N:67716	51		266117014	246797067	240014464	267491299	67716	SRX756916	SRS742120	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.92411	0.07686	0.68647	0.4627	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Kidney	Renal System
38297	38297	SRR1647680	SRX756915	SRS742117	SRP049663	PRJNA266803	Spring Varaemia of Carp Virus SVCV infection of adult zebrafish	GSE63133	Transcriptome Analysis	During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.		pubmed:25535281	6K	GSM1541904	source name:head kidney\|tissue:head kidney\|disease state:6h post SVCV infection	6K	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	head kidney		Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:head kidney\|disease state:6h post SVCV infection	GSM1541904	GSM1541904: 6K; Danio rerio; RNA Seq	GSM1541904		1	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1541904	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP049663		6K_GTCCGC_L003_R1.fastq	fastq	929436036.0	18224236.0	GSM1541904 r1	0:51	A:242005719;C:225485975;G:219890494;T:241993975;N:59873	51		242005719	225485975	219890494	241993975	59873	SRX756915	SRS742117	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.92547	0.09105	0.69264	0.49166	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Kidney	Renal System
38298	38298	SRR1647679	SRX756914	SRS742116	SRP049663	PRJNA266803	Spring Varaemia of Carp Virus SVCV infection of adult zebrafish	GSE63133	Transcriptome Analysis	During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.		pubmed:25535281	0K	GSM1541903	source name:head kidney\|tissue:head kidney\|disease state:un infected	0K	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	head kidney		Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:head kidney\|disease state:un infected	GSM1541903	GSM1541903: 0K; Danio rerio; RNA Seq	GSM1541903		1	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1541903	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP049663		0K_CCGTCC_L003_R1.fastq	fastq	1077979095.0	21136845.0	GSM1541903 r1	0:51	A:280277150;C:261348733;G:255721013;T:280562071;N:70128	51		280277150	261348733	255721013	280562071	70128	SRX756914	SRS742116	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.92545	0.08181	0.68373	0.49408	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Kidney	Renal System
41902	41902	SRR5337748	SRX2635098	SRS2043910	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378	YS6	GSM2534771	tissue:Mes1phros DL\|transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	YS6	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	Mesonephros DL		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	GSM2534771	GSM2534771: YS6; Danio rerio; RNA Seq	GSM2534771		1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534771	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756		20150717.A-YS6_R1.fastq.gz	fastq	5434051896.0	43127396.0	GSM2534771 r1	0:126	A:1185876928;C:1354521221;G:1643633065;T:1249907593;N:113089	126		1185876928	1354521221	1643633065	1249907593	113089	SRX2635098	SRS2043910	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.97351	0.17501	0.85303	0.75625	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41903	41903	SRR5337747	SRX2635097	SRS2043909	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378	YS5	GSM2534770	tissue:DL segments\|transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	YS5	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	DL segments		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	GSM2534770	GSM2534770: YS5; Danio rerio; RNA Seq	GSM2534770		1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534770	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756		20150717.A-YS5_R1.fastq(1).gz	fastq	2297696058.0	18235683.0	GSM2534770 r1	0:126	A:648837532;C:505738661;G:568578688;T:574489076;N:52101	126		648837532	505738661	568578688	574489076	52101	SRX2635097	SRS2043909	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.94402	0.1927	0.77585	0.67728	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41904	41904	SRR5337746	SRX2635096	SRS2043908	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378	YS4	GSM2534769	tissue:Mes1phros DL\|transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	YS4	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	Mesonephros DL		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	GSM2534769	GSM2534769: YS4; Danio rerio; RNA Seq	GSM2534769		1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534769	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756		20150717.A-YS4_R1.fastq.gz	fastq	4570634754.0	36274879.0	GSM2534769 r1	0:126	A:1179398927;C:1024363944;G:1239125274;T:1127644877;N:101732	126		1179398927	1024363944	1239125274	1127644877	101732	SRX2635096	SRS2043908	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.93083	0.27465	0.78102	0.70638	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41905	41905	SRR5337745	SRX2635095	SRS2043907	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378	YS3	GSM2534768	tissue:DL segments\|transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	YS3	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	DL segments		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	GSM2534768	GSM2534768: YS3; Danio rerio; RNA Seq	GSM2534768		1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534768	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756		20150717.A-YS3_R1.fastq.gz	fastq	5648398686.0	44828561.0	GSM2534768 r1	0:126	A:1607436982;C:1222995706;G:1369036558;T:1448805498;N:123942	126		1607436982	1222995706	1369036558	1448805498	123942	SRX2635095	SRS2043907	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.93399	0.20266	0.78076	0.73978	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41906	41906	SRR5337744	SRX2635094	SRS2043906	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378	YS2	GSM2534767	tissue:Mes1phros DL\|transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	YS2	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	Mesonephros DL		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	GSM2534767	GSM2534767: YS2; Danio rerio; RNA Seq	GSM2534767		1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534767	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756		20150717.A-YS2_R1.fastq.gz	fastq	4680679374.0	37148249.0	GSM2534767 r1	0:126	A:1320151433;C:986429614;G:1112497899;T:1261495719;N:104709	126		1320151433	986429614	1112497899	1261495719	104709	SRX2635094	SRS2043906	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.91952	0.24724	0.73884	0.63985	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41907	41907	SRR5337743	SRX2635093	SRS2043905	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378	YS1	GSM2534766	tissue:DL segments\|transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	YS1	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	DL segments		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	GSM2534766	GSM2534766: YS1; Danio rerio; RNA Seq	GSM2534766		1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534766	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756		20150717.A-YS1_R1.fastq.gz	fastq	7000703892.0	55561142.0	GSM2534766 r1	0:126	A:1521231890;C:1760818628;G:2148863730;T:1569634203;N:155441	126		1521231890	1760818628	2148863730	1569634203	155441	SRX2635093	SRS2043905	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.96016	0.1982	0.86261	0.75572	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
42599	42599	SRR5810682	SRX2989237	SRS2341160	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of multiple samples 2	GSM2696104	source name:Whole kidney marrow\|indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	inDrop sequencing of multiple samples 2	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	GSM2696104	GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq	GSM2696104		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696104	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		inDrop_v3_run2_R1.fastq.gz	fastq	23315853588.0	382227108.0	GSM2696104 r1	0:61 1:0	A:6573828142;C:5137891481;G:5021324431;T:6582457296;N:352238	61	0	6573828142	5137891481	5021324431	6582457296	352238	SRX2989237	SRS2341160	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.83828	0.08537	0.83552	0.56658	61	B	usable mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42600	42600	SRR5810683	SRX2989237	SRS2341160	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of multiple samples 2	GSM2696104	source name:Whole kidney marrow\|indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	inDrop sequencing of multiple samples 2	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	GSM2696104	GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq	GSM2696104		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696104	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		inDrop_v3_run2_R2.fastq.gz	fastq	3057816864.0	382227108.0	GSM2696104 r2	0:0 1:8	A:743619897;C:720488231;G:1031094190;T:562297818;N:316728	0	8	743619897	720488231	1031094190	562297818	316728	SRX2989237	SRS2341160	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.0	0.0	1.0		8	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42601	42601	SRR5810684	SRX2989237	SRS2341160	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of multiple samples 2	GSM2696104	source name:Whole kidney marrow\|indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	inDrop sequencing of multiple samples 2	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	GSM2696104	GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq	GSM2696104		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696104	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		inDrop_v3_run2_R3.fastq.gz	fastq	3057816864.0	382227108.0	GSM2696104 r3	0:8	A:913664473;C:577895371;G:646194239;T:918893384;N:1169397	8		913664473	577895371	646194239	918893384	1169397	SRX2989237	SRS2341160	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.0	0.0	1.0		8	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42602	42602	SRR5810685	SRX2989237	SRS2341160	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of multiple samples 2	GSM2696104	source name:Whole kidney marrow\|indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	inDrop sequencing of multiple samples 2	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	GSM2696104	GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq	GSM2696104		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696104	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		inDrop_v3_run2_R4.fastq.gz	fastq	5351179512.0	382227108.0	GSM2696104 r4	0:14	A:1351470715;C:1294400719;G:1379073889;T:1322397488;N:3836701	14		1351470715	1294400719	1379073889	1322397488	3836701	SRX2989237	SRS2341160	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.0	0.0	1.0		14	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42603	42603	SRR5810678	SRX2989236	SRS2341159	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of multiple samples 1	GSM2696103	source name:Whole kidney marrow\|indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	inDrop sequencing of multiple samples 1	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	GSM2696103	GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq	GSM2696103		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696103	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		inDrop_v3_run1_R1.fastq.gz	fastq	26868371039.0	440465099.0	GSM2696103 r1	0:61 1:0	A:7598044404;C:5948542485;G:5746339343;T:7575168754;N:276053	61	0	7598044404	5948542485	5746339343	7575168754	276053	SRX2989236	SRS2341159	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.83437	0.08222	0.82658	0.54569	61	B	usable mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42604	42604	SRR5810679	SRX2989236	SRS2341159	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of multiple samples 1	GSM2696103	source name:Whole kidney marrow\|indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	inDrop sequencing of multiple samples 1	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	GSM2696103	GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq	GSM2696103		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696103	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		inDrop_v3_run1_R2.fastq.gz	fastq	3523720792.0	440465099.0	GSM2696103 r2	0:0 1:8	A:892841722;C:781074758;G:1176856476;T:672376743;N:571093	0	8	892841722	781074758	1176856476	672376743	571093	SRX2989236	SRS2341159	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.0	0.0	1.0		8	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42605	42605	SRR5810680	SRX2989236	SRS2341159	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of multiple samples 1	GSM2696103	source name:Whole kidney marrow\|indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	inDrop sequencing of multiple samples 1	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	GSM2696103	GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq	GSM2696103		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696103	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		inDrop_v3_run1_R3.fastq.gz	fastq	3523720792.0	440465099.0	GSM2696103 r3	0:8	A:1016854893;C:682256486;G:759860179;T:1063129659;N:1619575	8		1016854893	682256486	759860179	1063129659	1619575	SRX2989236	SRS2341159	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.0	0.0	1.0		8	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42606	42606	SRR5810681	SRX2989236	SRS2341159	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of multiple samples 1	GSM2696103	source name:Whole kidney marrow\|indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	inDrop sequencing of multiple samples 1	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V3 protocol\|tissue:kidney marrow\|genotype:multiple genotypes	GSM2696103	GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq	GSM2696103		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696103	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		inDrop_v3_run1_R4.fastq.gz	fastq	6166511386.0	440465099.0	GSM2696103 r4	0:14	A:1513770161;C:1469643118;G:1669791951;T:1509862301;N:3443855	14		1513770161	1469643118	1669791951	1509862301	3443855	SRX2989236	SRS2341159	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.0	0.0	1.0		14	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42607	42607	SRR5810676	SRX2989235	SRS2341158	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2	GSM2696102	source name:Whole kidney marrow\|indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:prkdcD3612fs	inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:prkdcD3612fs	GSM2696102	GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq	GSM2696102		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696102	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		PRKDC2_R1.fastq.gz	fastq	1987929396.0	55220261.0	GSM2696102 r1	0:36 1:0	A:506372087;C:413396954;G:415448050;T:652683387;N:28918	36	0	506372087	413396954	415448050	652683387	28918	SRX2989235	SRS2341158	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.86587	0.12447	0.80336	0.54126	36	B	usable mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42608	42608	SRR5810677	SRX2989235	SRS2341158	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2	GSM2696102	source name:Whole kidney marrow\|indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:prkdcD3612fs	inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:prkdcD3612fs	GSM2696102	GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq	GSM2696102		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696102	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		PRKDC2_R2.fastq.gz	fastq	2761013050.0	55220261.0	GSM2696102 r2	0:0 1:50	A:554483675;C:506568509;G:721419849;T:974751566;N:3789451	0	50	554483675	506568509	721419849	974751566	3789451	SRX2989235	SRS2341158	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.00796	0.0077	0.99961	0.78947	50	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42609	42609	SRR5810674	SRX2989234	SRS2341157	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1	GSM2696101	source name:Whole kidney marrow\|indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:prkdcD3612fs	inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:prkdcD3612fs	GSM2696101	GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq	GSM2696101		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696101	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		PRKDC1_R1.fastq.gz	fastq	1549442736.0	43040076.0	GSM2696101 r1	0:36 1:0	A:402261661;C:326108405;G:319637981;T:501413963;N:20726	36	0	402261661	326108405	319637981	501413963	20726	SRX2989234	SRS2341157	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.84263	0.11449	0.79464	0.57001	36	B	usable mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42610	42610	SRR5810675	SRX2989234	SRS2341157	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1	GSM2696101	source name:Whole kidney marrow\|indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:prkdcD3612fs	inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:prkdcD3612fs	GSM2696101	GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq	GSM2696101		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696101	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		PRKDC1_R2.fastq.gz	fastq	2152003800.0	43040076.0	GSM2696101 r2	0:0 1:50	A:432547886;C:403759182;G:561234660;T:751564536;N:2897536	0	50	432547886	403759182	561234660	751564536	2897536	SRX2989234	SRS2341157	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.00796	0.00773	0.99971	0.82758	50	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42611	42611	SRR5810672	SRX2989233	SRS2341156	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of WT sample animal #2	GSM2696100	source name:Whole kidney marrow\|indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:wildtype	inDrop sequencing of WT sample animal #2	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:wildtype	GSM2696100	GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq	GSM2696100		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696100	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		WT2_R1.fastq.gz	fastq	3202042500.0	88945625.0	GSM2696100 r1	0:36 1:0	A:821476951;C:657776656;G:665293293;T:1057448635;N:46965	36	0	821476951	657776656	665293293	1057448635	46965	SRX2989233	SRS2341156	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.84222	0.12969	0.80683	0.53542	36	B	usable mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42612	42612	SRR5810673	SRX2989233	SRS2341156	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of WT sample animal #2	GSM2696100	source name:Whole kidney marrow\|indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:wildtype	inDrop sequencing of WT sample animal #2	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:wildtype	GSM2696100	GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq	GSM2696100		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696100	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		WT2_R2.fastq.gz	fastq	4447281250.0	88945625.0	GSM2696100 r2	0:0 1:50	A:880464480;C:827380868;G:1171423978;T:1561925150;N:6086774	0	50	880464480	827380868	1171423978	1561925150	6086774	SRX2989233	SRS2341156	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.00782	0.0075	0.99947	0.91666	50	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42613	42613	SRR5810670	SRX2989232	SRS2341155	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of WT sample animal #1	GSM2696099	source name:Whole kidney marrow\|indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:wildtype	inDrop sequencing of WT sample animal #1	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:wildtype	GSM2696099	GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq	GSM2696099		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696099	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		WT1_R1.fastq.gz	fastq	3313205496.0	92033486.0	GSM2696099 r1	0:36 1:0	A:858288917;C:693848400;G:675650809;T:1085369048;N:48322	36	0	858288917	693848400	675650809	1085369048	48322	SRX2989232	SRS2341155	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.8771	0.13918	0.81115	0.59004	36	B	usable mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
42614	42614	SRR5810671	SRX2989232	SRS2341155	SRP111339	PRJNA393429	Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]	GSE100910	Transcriptome Analysis	Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals …	parent bioproject:PRJNA393415	pubmed:28878000	inDrop sequencing of WT sample animal #1	GSM2696099	source name:Whole kidney marrow\|indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:wildtype	inDrop sequencing of WT sample animal #1	Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.	Whole kidney marrow		RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.		indrop version:inDrop V2 protocol\|tissue:kidney marrow\|genotype:wildtype	GSM2696099	GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq	GSM2696099		1	RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.	GEO Accession:GSM2696099	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP111339		WT1_R2.fastq.gz	fastq	4601674300.0	92033486.0	GSM2696099 r2	0:0 1:50	A:914884703;C:856837987;G:1192418010;T:1631240786;N:6292814	0	50	914884703	856837987	1192418010	1631240786	6292814	SRX2989232	SRS2341155	SRA584587	GEO	Pathology, Massachusetts General Hospital	1	0.0063	0.00598	0.99959	0.8913	50	T	under 1.2% mapping rate	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2017-07-07	Undetermined	Adult	Kidney	Renal System
47595	47595	SRR6661145	SRX3638241	SRS2904492	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidWTPHZ 3	GSM2975189	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	KidWTPHZ 3	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975189	GSM2975189: KidWTPHZ 3; Danio rerio; RNA Seq	GSM2975189		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975189	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidWTPHZ_3.fastq.gz	fastq	858099990.0	16825490.0	GSM2975189 r1	0:51	A:231903062;C:197865548;G:200825484;T:227491985;N:13911	51		231903062	197865548	200825484	227491985	13911	SRX3638241	SRS2904492	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.9605	0.10316	0.70721	0.51089	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47596	47596	SRR6661144	SRX3638240	SRS2904491	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidWTPHZ 2	GSM2975188	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	KidWTPHZ 2	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975188	GSM2975188: KidWTPHZ 2; Danio rerio; RNA Seq	GSM2975188		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975188	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidWTPHZ_2.fastq.gz	fastq	799571013.0	15677863.0	GSM2975188 r1	0:51	A:217401512;C:183178629;G:185275617;T:213702318;N:12937	51		217401512	183178629	185275617	213702318	12937	SRX3638240	SRS2904491	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.96209	0.10882	0.70861	0.5149	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47597	47597	SRR6661143	SRX3638239	SRS2904490	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidWTPHZ 1	GSM2975187	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	KidWTPHZ 1	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975187	GSM2975187: KidWTPHZ 1; Danio rerio; RNA Seq	GSM2975187		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975187	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidWTPHZ_1.fastq.gz	fastq	816038505.0	16000755.0	GSM2975187 r1	0:51	A:218420574;C:190260181;G:192288409;T:215056318;N:13023	51		218420574	190260181	192288409	215056318	13023	SRX3638239	SRS2904490	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.96264	0.09527	0.70834	0.51477	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47598	47598	SRR6661142	SRX3638238	SRS2904489	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidWT 3	GSM2975186	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	KidWT 3	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975186	GSM2975186: KidWT 3; Danio rerio; RNA Seq	GSM2975186		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975186	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidWT_3.fastq.gz	fastq	852094026.0	16707726.0	GSM2975186 r1	0:51	A:234167802;C:192807979;G:194651214;T:230453461;N:13570	51		234167802	192807979	194651214	230453461	13570	SRX3638238	SRS2904489	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.95788	0.12336	0.70258	0.48964	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47599	47599	SRR6661141	SRX3638237	SRS2904488	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidWT 2	GSM2975185	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	KidWT 2	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975185	GSM2975185: KidWT 2; Danio rerio; RNA Seq	GSM2975185		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975185	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidWT_2.fastq.gz	fastq	969772038.0	19015138.0	GSM2975185 r1	0:51	A:265582126;C:219526888;G:222468938;T:262178447;N:15639	51		265582126	219526888	222468938	262178447	15639	SRX3638237	SRS2904488	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.95803	0.12522	0.69794	0.50805	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47600	47600	SRR6661140	SRX3638236	SRS2904487	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidWT 1	GSM2975184	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	KidWT 1	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975184	GSM2975184: KidWT 1; Danio rerio; RNA Seq	GSM2975184		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975184	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidWT_1.fastq.gz	fastq	815590011.0	15991961.0	GSM2975184 r1	0:51	A:224190865;C:184406547;G:186159880;T:220819162;N:13557	51		224190865	184406547	186159880	220819162	13557	SRX3638236	SRS2904487	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.95883	0.13181	0.7023	0.49523	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47601	47601	SRR6661139	SRX3638235	SRS2904486	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidDKOPHZ 3	GSM2975183	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	KidDKOPHZ 3	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975183	GSM2975183: KidDKOPHZ 3; Danio rerio; RNA Seq	GSM2975183		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975183	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidDKOPHZ_3.fastq.gz	fastq	789588885.0	15482135.0	GSM2975183 r1	0:51	A:215354577;C:180286176;G:181162894;T:212772248;N:12990	51		215354577	180286176	181162894	212772248	12990	SRX3638235	SRS2904486	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.92385	0.10405	0.70471	0.50985	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47602	47602	SRR6661138	SRX3638234	SRS2904485	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidDKOPHZ 2	GSM2975182	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	KidDKOPHZ 2	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975182	GSM2975182: KidDKOPHZ 2; Danio rerio; RNA Seq	GSM2975182		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975182	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidDKOPHZ_2.fastq.gz	fastq	866844552.0	16996952.0	GSM2975182 r1	0:51	A:235445628;C:198901971;G:200334068;T:232148841;N:14044	51		235445628	198901971	200334068	232148841	14044	SRX3638234	SRS2904485	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.92657	0.10886	0.71112	0.52093	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47603	47603	SRR6661137	SRX3638233	SRS2904484	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidDKOPHZ 1	GSM2975181	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	KidDKOPHZ 1	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975181	GSM2975181: KidDKOPHZ 1; Danio rerio; RNA Seq	GSM2975181		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975181	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidDKOPHZ_1.fastq.gz	fastq	795526560.0	15598560.0	GSM2975181 r1	0:51	A:216666052;C:181785239;G:183159054;T:213903089;N:13126	51		216666052	181785239	183159054	213903089	13126	SRX3638233	SRS2904484	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.92522	0.10277	0.7121	0.51721	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47604	47604	SRR6661136	SRX3638232	SRS2904483	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidDKO 3	GSM2975180	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	KidDKO 3	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975180	GSM2975180: KidDKO 3; Danio rerio; RNA Seq	GSM2975180		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975180	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidDKO_3.fastq.gz	fastq	699170577.0	13709227.0	GSM2975180 r1	0:51	A:191094810;C:157413925;G:158857752;T:191792628;N:11462	51		191094810	157413925	158857752	191792628	11462	SRX3638232	SRS2904483	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.9183	0.12207	0.7083	0.52994	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47605	47605	SRR6661135	SRX3638231	SRS2904482	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidDKO 2	GSM2975179	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	KidDKO 2	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975179	GSM2975179: KidDKO 2; Danio rerio; RNA Seq	GSM2975179		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975179	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidDKO_2.fastq.gz	fastq	720757194.0	14132494.0	GSM2975179 r1	0:51	A:198433339;C:163064446;G:163967236;T:195280391;N:11782	51		198433339	163064446	163967236	195280391	11782	SRX3638231	SRS2904482	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.92921	0.11261	0.7063	0.52644	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
47606	47606	SRR6661134	SRX3638230	SRS2904481	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.		pubmed:30248094	KidDKO 1	GSM2975178	source name:whole animal\|tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	KidDKO 1	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:kidney\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975178	GSM2975178: KidDKO 1; Danio rerio; RNA Seq	GSM2975178		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975178	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP131956		KidDKO_1.fastq.gz	fastq	835548606.0	16383306.0	GSM2975178 r1	0:51	A:227900020;C:191118125;G:192603640;T:223913065;N:13756	51		227900020	191118125	192603640	223913065	13756	SRX3638230	SRS2904481	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.93166	0.10926	0.7063	0.50705	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Kidney	Renal System
48941	48941	SRR7535399	SRX4403259	SRS3557748	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample43	F3HFL6	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3HFL6 L43	F3HFL6 L43	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3HFL6.fastq.gz	fastq	3513906206.0	41769622.0	F3HFL6.fastq.gz	0:84.13 1:0	A:977114573;C:787720805;G:749651347;T:999364818;N:54663	84	0	977114573	787720805	749651347	999364818	54663	SRX4403259	SRS3557748	SRA741696	Gov of Canada	Gov of Canada	1	0.95671	0.06506	0.78228	0.56305	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48942	48942	SRR7535400	SRX4403258	SRS3557747	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample41	F3HFL4	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3HFL4 L41	F3HFL4 L41	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3HFL4.fastq.gz	fastq	1925799513.0	22885356.0	F3HFL4.fastq.gz	0:84.15 1:0	A:524298249;C:430610288;G:398055851;T:572803437;N:31688	84	0	524298249	430610288	398055851	572803437	31688	SRX4403258	SRS3557747	SRA741696	Gov of Canada	Gov of Canada	1	0.93737	0.10113	0.81022	0.55692	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48943	48943	SRR7535401	SRX4403257	SRS3557746	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample42	F3HFL5	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3HFL5 L42	F3HFL5 L42	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3HFL5.fastq.gz	fastq	2861742645.0	33977477.0	F3HFL5.fastq.gz	0:84.22 1:0	A:771306767;C:644570838;G:600324085;T:845486554;N:54401	84	0	771306767	644570838	600324085	845486554	54401	SRX4403257	SRS3557746	SRA741696	Gov of Canada	Gov of Canada	1	0.95145	0.08188	0.78084	0.53906	82	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-07-18	Adult	Adult	Kidney	Renal System
48944	48944	SRR7535402	SRX4403256	SRS3557745	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample21	F0HFL8	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0HFL8 L21	F0HFL8 L21	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0HFL8.fastq.gz	fastq	3270195567.0	43558704.0	F0HFL8.fastq.gz	0:75.08 1:0	A:931015183;C:710121529;G:674934313;T:954020799;N:103743	75	0	931015183	710121529	674934313	954020799	103743	SRX4403256	SRS3557745	SRA741696	Gov of Canada	Gov of Canada	1	0.94496	0.07696	0.74931	0.55469	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48945	48945	SRR7535403	SRX4403255	SRS3557744	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample22	F3CTR1	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3CTR1 L22	F3CTR1 L22	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3CTR1.fastq.gz	fastq	2224836049.0	29606943.0	F3CTR1.fastq.gz	0:75.15 1:0	A:610515696;C:506550058;G:471139873;T:636560130;N:70292	75	0	610515696	506550058	471139873	636560130	70292	SRX4403255	SRS3557744	SRA741696	Gov of Canada	Gov of Canada	1	0.95447	0.0754	0.78066	0.54856	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48946	48946	SRR7535404	SRX4403254	SRS3557743	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample23	F3CTR2	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3CTR2 L23	F3CTR2 L23	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3CTR2.fastq.gz	fastq	3106167820.0	36871227.0	F3CTR2.fastq.gz	0:84.24 1:0	A:844192333;C:713285812;G:657110592;T:891518698;N:60385	84	0	844192333	713285812	657110592	891518698	60385	SRX4403254	SRS3557743	SRA741696	Gov of Canada	Gov of Canada	1	0.9554	0.06997	0.79275	0.52557	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48947	48947	SRR7535405	SRX4403253	SRS3557742	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample24	F3CTR3	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3CTR3 L24	F3CTR3 L24	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3CTR3.fastq.gz	fastq	2619378393.0	31091747.0	F3CTR3.fastq.gz	0:84.25 1:0	A:699692748;C:600624113;G:564410765;T:754600796;N:49971	84	0	699692748	600624113	564410765	754600796	49971	SRX4403253	SRS3557742	SRA741696	Gov of Canada	Gov of Canada	1	0.95974	0.06076	0.7932	0.54096	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48948	48948	SRR7535406	SRX4403252	SRS3557741	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample25	F3CTR4	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3CTR4 L25	F3CTR4 L25	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3CTR4.fastq.gz	fastq	3292260052.0	39078900.0	F3CTR4.fastq.gz	0:84.25 1:0	A:880017890;C:753064780;G:705989117;T:953125639;N:62626	84	0	880017890	753064780	705989117	953125639	62626	SRX4403252	SRS3557741	SRA741696	Gov of Canada	Gov of Canada	1	0.95321	0.07242	0.75666	0.54587	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48949	48949	SRR7535407	SRX4403251	SRS3557740	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample26	F3CTR5	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3CTR5 L26	F3CTR5 L26	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3CTR5.fastq.gz	fastq	3007976354.0	35696121.0	F3CTR5.fastq.gz	0:84.27 1:0	A:778578191;C:708292962;G:650565998;T:870481710;N:57493	84	0	778578191	708292962	650565998	870481710	57493	SRX4403251	SRS3557740	SRA741696	Gov of Canada	Gov of Canada	1	0.95344	0.06722	0.7597	0.52143	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48950	48950	SRR7535408	SRX4403250	SRS3557739	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample27	F3CTR6	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3CTR6 L27	F3CTR6 L27	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3CTR6.fastq.gz	fastq	2550867627.0	31161224.0	F3CTR6.fastq.gz	0:81.86 1:0	A:1115959207;C:419324274;G:453781546;T:561761915;N:40685	81	0	1115959207	419324274	453781546	561761915	40685	SRX4403250	SRS3557739	SRA741696	Gov of Canada	Gov of Canada	1	0.92888	0.24434	0.77749	0.51629	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48951	48951	SRR7535409	SRX4403249	SRS3557738	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample28	F3CTR7	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3CTR7 L28	F3CTR7 L28	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3CTR7.fastq.gz	fastq	2059768786.0	24468469.0	F3CTR7.fastq.gz	0:84.18 1:0	A:558059300;C:468460643;G:436031484;T:597176496;N:40863	84	0	558059300	468460643	436031484	597176496	40863	SRX4403249	SRS3557738	SRA741696	Gov of Canada	Gov of Canada	1	0.94686	0.07284	0.77459	0.54014	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48952	48952	SRR7535410	SRX4403248	SRS3557737	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample29	F3CTR8	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3CTR8 L29	F3CTR8 L29	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3CTR8.fastq.gz	fastq	3053213414.0	36279614.0	F3CTR8.fastq.gz	0:84.16 1:0	A:815581740;C:713814496;G:673475187;T:850294355;N:47636	84	0	815581740	713814496	673475187	850294355	47636	SRX4403248	SRS3557737	SRA741696	Gov of Canada	Gov of Canada	1	0.9571	0.06714	0.75369	0.54721	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48953	48953	SRR7535411	SRX4403247	SRS3557736	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample30	F3LFL1	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3LFL1 L30	F3LFL1 L30	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3LFL1.fastq.gz	fastq	2028343411.0	26987895.0	F3LFL1.fastq.gz	0:75.16 1:0	A:548593649;C:466971074;G:433327481;T:579386722;N:64485	75	0	548593649	466971074	433327481	579386722	64485	SRX4403247	SRS3557736	SRA741696	Gov of Canada	Gov of Canada	1	0.95498	0.0741	0.7895	0.5309	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-07-18	Adult	Adult	Kidney	Renal System
48954	48954	SRR7535412	SRX4403246	SRS3557735	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample8	F0CTR8	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0CTR8 L8	F0CTR8 L8	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0CTR8.fastq.gz	fastq	2222889019.0	29574868.0	F0CTR8.fastq.gz	0:75.16 1:0	A:596733500;C:518690507;G:486721856;T:620675208;N:67948	75	0	596733500	518690507	486721856	620675208	67948	SRX4403246	SRS3557735	SRA741696	Gov of Canada	Gov of Canada	1	0.95446	0.05545	0.74815	0.51889	74	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48955	48955	SRR7535413	SRX4403245	SRS3557734	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample7	F0CTR7	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0CTR7 L7	F0CTR7 L7	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0CTR7.fastq.gz	fastq	4544318503.0	53947186.0	F0CTR7.fastq.gz	0:84.24 1:0	A:1292030811;C:991354554;G:942494048;T:1318393334;N:45756	84	0	1292030811	991354554	942494048	1318393334	45756	SRX4403245	SRS3557734	SRA741696	Gov of Canada	Gov of Canada	1	0.9503	0.06778	0.75743	0.55348	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-07-18	Adult	Adult	Kidney	Renal System
48956	48956	SRR7535414	SRX4403244	SRS3557733	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample6	F0CTR6	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0CTR6 L6	F0CTR6 L6	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0CTR6.fastq.gz	fastq	2358891923.0	31391321.0	F0CTR6.fastq.gz	0:75.14 1:0	A:685288644;C:509459791;G:472389125;T:691678243;N:76120	75	0	685288644	509459791	472389125	691678243	76120	SRX4403244	SRS3557733	SRA741696	Gov of Canada	Gov of Canada	1	0.94166	0.07795	0.76195	0.53942	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48957	48957	SRR7535415	SRX4403243	SRS3557732	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample5	F0CTR5	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0CTR5 L5	F0CTR5 L5	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0CTR5.fastq.gz	fastq	2588676344.0	30755117.0	F0CTR5.fastq.gz	0:84.17 1:0	A:720655179;C:582123937;G:551878210;T:733977893;N:41125	84	0	720655179	582123937	551878210	733977893	41125	SRX4403243	SRS3557732	SRA741696	Gov of Canada	Gov of Canada	1	0.95586	0.06561	0.7808	0.54698	83	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48958	48958	SRR7535416	SRX4403242	SRS3557731	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample4	F0CTR4	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0CTR4 L4	F0CTR4 L4	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0CTR4.fastq.gz	fastq	2959885275.0	35175450.0	F0CTR4.fastq.gz	0:84.15 1:0	A:799876836;C:675392846;G:616854860;T:867718008;N:42725	84	0	799876836	675392846	616854860	867718008	42725	SRX4403242	SRS3557731	SRA741696	Gov of Canada	Gov of Canada	1	0.93974	0.07556	0.76238	0.50131	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48959	48959	SRR7535417	SRX4403241	SRS3557730	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample3	F0CTR3	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0CTR3 L3	F0CTR3 L3	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0CTR3.fastq.gz	fastq	3127991402.0	37019173.0	F0CTR3.fastq.gz	0:84.50 1:0	A:886233117;C:699410395;G:659031655;T:883271353;N:44882	84	0	886233117	699410395	659031655	883271353	44882	SRX4403241	SRS3557730	SRA741696	Gov of Canada	Gov of Canada	1	0.95481	0.06332	0.77818	0.54263	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48960	48960	SRR7535418	SRX4403240	SRS3557729	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample2	F0CTR2	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0CTR2 L2	F0CTR2 L2	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0CTR2.fastq.gz	fastq	4589246236.0	54480219.0	F0CTR2.fastq.gz	0:84.24 1:0	A:1318726005;C:987643623;G:940290206;T:1342543647;N:42755	84	0	1318726005	987643623	940290206	1342543647	42755	SRX4403240	SRS3557729	SRA741696	Gov of Canada	Gov of Canada	1	0.94686	0.06888	0.76278	0.55045	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48961	48961	SRR7535419	SRX4403239	SRS3557728	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample1	F0CTR1	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0CTR1 L1	F0CTR1 L1	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0CTR1.fastq.gz	fastq	2895973720.0	34407735.0	F0CTR1.fastq.gz	0:84.17 1:0	A:805217942;C:647195655;G:615425828;T:828086852;N:47443	84	0	805217942	647195655	615425828	828086852	47443	SRX4403239	SRS3557728	SRA741696	Gov of Canada	Gov of Canada	1	0.95771	0.05823	0.75475	0.54018	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-07-18	Adult	Adult	Kidney	Renal System
48962	48962	SRR7535420	SRX4403238	SRS3557727	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample10	F0LFL2	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0LFL2 L10	F0LFL2 L10	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0LFL2.fastq.gz	fastq	2221964224.0	29564609.0	F0LFL2.fastq.gz	0:75.16 1:0	A:622205890;C:491850489;G:469917376;T:637922036;N:68433	75	0	622205890	491850489	469917376	637922036	68433	SRX4403238	SRS3557727	SRA741696	Gov of Canada	Gov of Canada	1	0.95207	0.06132	0.76404	0.5374	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48963	48963	SRR7535421	SRX4403237	SRS3557726	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample9	F0LFL1	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0LFL1 L9	F0LFL1 L9	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0LFL1.fastq.gz	fastq	3222133895.0	38154313.0	F0LFL1.fastq.gz	0:84.45 1:0	A:920033678;C:715675242;G:671297913;T:915080329;N:46733	84	0	920033678	715675242	671297913	915080329	46733	SRX4403237	SRS3557726	SRA741696	Gov of Canada	Gov of Canada	1	0.95496	0.07355	0.76644	0.54508	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48964	48964	SRR7535422	SRX4403236	SRS3557725	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample20	F0HFL7	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0HFL7 L20	F0HFL7 L20	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0HFL7.fastq.gz	fastq	2800528980.0	33270152.0	F0HFL7.fastq.gz	0:84.18 1:0	A:745732773;C:657771159;G:624594638;T:772385369;N:45041	84	0	745732773	657771159	624594638	772385369	45041	SRX4403236	SRS3557725	SRA741696	Gov of Canada	Gov of Canada	1	0.9603	0.05557	0.75262	0.53229	83	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48965	48965	SRR7535423	SRX4403235	SRS3557724	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample19	F0HFL6	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0HFL6 L19	F0HFL6 L19	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0HFL6.fastq.gz	fastq	3859582889.0	45819776.0	F0HFL6.fastq.gz	0:84.23 1:0	A:1042286597;C:895964648;G:843235146;T:1078059877;N:36621	84	0	1042286597	895964648	843235146	1078059877	36621	SRX4403235	SRS3557724	SRA741696	Gov of Canada	Gov of Canada	1	0.95288	0.06929	0.74	0.52268	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48966	48966	SRR7535424	SRX4403234	SRS3557723	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample16	F0HFL3	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0HFL3 L16	F0HFL3 L16	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0HFL3.fastq.gz	fastq	3793212903.0	45071794.0	F0HFL3.fastq.gz	0:84.16 1:0	A:1056360853;C:843514256;G:810627279;T:1082649387;N:61128	84	0	1056360853	843514256	810627279	1082649387	61128	SRX4403234	SRS3557723	SRA741696	Gov of Canada	Gov of Canada	1	0.95323	0.06159	0.76195	0.54295	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48967	48967	SRR7535425	SRX4403233	SRS3557722	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample15	F0HFL2	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0HFL2 L15	F0HFL2 L15	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0HFL2.fastq.gz	fastq	1653605409.0	19670232.0	F0HFL2.fastq.gz	0:84.07 1:0	A:482659933;C:340033054;G:332925206;T:497960425;N:26791	84	0	482659933	340033054	332925206	497960425	26791	SRX4403233	SRS3557722	SRA741696	Gov of Canada	Gov of Canada	1	0.94378	0.07818	0.76654	0.56019	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48968	48968	SRR7535426	SRX4403232	SRS3557721	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample18	F0HFL5	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0HFL5 L18	F0HFL5 L18	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0HFL5.fastq.gz	fastq	2841372173.0	33797215.0	F0HFL5.fastq.gz	0:84.07 1:0	A:778391982;C:632117929;G:585902045;T:844912619;N:47598	84	0	778391982	632117929	585902045	844912619	47598	SRX4403232	SRS3557721	SRA741696	Gov of Canada	Gov of Canada	1	0.93559	0.07561	0.76895	0.55817	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48969	48969	SRR7535427	SRX4403231	SRS3557719	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample17	F0HFL4	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0HFL4 L17	F0HFL4 L17	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0HFL4.fastq.gz	fastq	3160174261.0	37565835.0	F0HFL4.fastq.gz	0:84.12 1:0	A:884296991;C:697282059;G:667815635;T:910728716;N:50860	84	0	884296991	697282059	667815635	910728716	50860	SRX4403231	SRS3557719	SRA741696	Gov of Canada	Gov of Canada	1	0.95258	0.06896	0.75753	0.53648	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48970	48970	SRR7535428	SRX4403230	SRS3557720	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample12	F0LFL4	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0LFL4 L12	F0LFL4 L12	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0LFL4.fastq.gz	fastq	2872309444.0	34017640.0	F0LFL4.fastq.gz	0:84.44 1:0	A:838123566;C:615148814;G:580099793;T:838897200;N:40071	84	0	838123566	615148814	580099793	838897200	40071	SRX4403230	SRS3557720	SRA741696	Gov of Canada	Gov of Canada	1	0.94655	0.07484	0.76055	0.53193	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48971	48971	SRR7535429	SRX4403229	SRS3557718	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample11	F0LFL3	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0LFL3 L11	F0LFL3 L11	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0LFL3.fastq.gz	fastq	4819656374.0	57208863.0	F0LFL3.fastq.gz	0:84.25 1:0	A:1344664833;C:1065935819;G:1021114550;T:1387895714;N:45458	84	0	1344664833	1065935819	1021114550	1387895714	45458	SRX4403229	SRS3557718	SRA741696	Gov of Canada	Gov of Canada	1	0.94968	0.06704	0.75063	0.53941	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48972	48972	SRR7535430	SRX4403228	SRS3557717	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample14	F0HFL1	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0HFL1 L14	F0HFL1 L14	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0HFL1.fastq.gz	fastq	4382160649.0	58413517.0	F0HFL1.fastq.gz	0:75.02 1:0	A:1369437301;C:861646512;G:809593345;T:1341341422;N:142069	75	0	1369437301	861646512	809593345	1341341422	142069	SRX4403228	SRS3557717	SRA741696	Gov of Canada	Gov of Canada	1	0.9466	0.08719	0.7794	0.54372	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-07-18	Adult	Adult	Kidney	Renal System
48973	48973	SRR7535431	SRX4403227	SRS3557716	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample13	F0LFL5	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F0LFL5 L13	F0LFL5 L13	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F0LFL5.fastq.gz	fastq	4135324561.0	55077889.0	F0LFL5.fastq.gz	0:75.08 1:0	A:1152758595;C:923324532;G:883060803;T:1176048511;N:132120	75	0	1152758595	923324532	883060803	1176048511	132120	SRX4403227	SRS3557716	SRA741696	Gov of Canada	Gov of Canada	1	0.94936	0.07427	0.7385	0.54293	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48974	48974	SRR7535432	SRX4403226	SRS3557715	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample38	F3HFL1	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3HFL1 L38	F3HFL1 L38	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3HFL1.fastq.gz	fastq	4205002265.0	49802474.0	F3HFL1.fastq.gz	0:84.43 1:0	A:1296210304;C:849397168;G:835453941;T:1223875076;N:65776	84	0	1296210304	849397168	835453941	1223875076	65776	SRX4403226	SRS3557715	SRA741696	Gov of Canada	Gov of Canada	1	0.95559	0.0917	0.78044	0.61361	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48975	48975	SRR7535433	SRX4403225	SRS3557714	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample37	F3LFL8	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3LFL8 L37	F3LFL8 L37	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3LFL8.fastq.gz	fastq	2259705259.0	26829092.0	F3LFL8.fastq.gz	0:84.23 1:0	A:609862793;C:515167321;G:475663194;T:658969872;N:42079	84	0	609862793	515167321	475663194	658969872	42079	SRX4403225	SRS3557714	SRA741696	Gov of Canada	Gov of Canada	1	0.94002	0.10434	0.75369	0.51155	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48976	48976	SRR7535434	SRX4403224	SRS3557713	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample36	F3LFL7	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3LFL7 L36	F3LFL7 L36	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3LFL7.fastq.gz	fastq	2341138815.0	27781759.0	F3LFL7.fastq.gz	0:84.27 1:0	A:608466569;C:545924123;G:501493228;T:685210306;N:44589	84	0	608466569	545924123	501493228	685210306	44589	SRX4403224	SRS3557713	SRA741696	Gov of Canada	Gov of Canada	1	0.94523	0.08263	0.75284	0.53752	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48977	48977	SRR7535435	SRX4403223	SRS3557712	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample35	F3LFL6	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3LFL6 L35	F3LFL6 L35	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3LFL6.fastq.gz	fastq	2937598885.0	34879736.0	F3LFL6.fastq.gz	0:84.22 1:0	A:782454526;C:678806792;G:617210082;T:859072883;N:54602	84	0	782454526	678806792	617210082	859072883	54602	SRX4403223	SRS3557712	SRA741696	Gov of Canada	Gov of Canada	1	0.94207	0.08495	0.74897	0.5069	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48978	48978	SRR7535436	SRX4403222	SRS3557711	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample34	F3LFL5	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3LFL5 L34	F3LFL5 L34	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3LFL5.fastq.gz	fastq	2497066825.0	29658022.0	F3LFL5.fastq.gz	0:84.20 1:0	A:694874960;C:555774576;G:516525097;T:729844057;N:48135	84	0	694874960	555774576	516525097	729844057	48135	SRX4403222	SRS3557711	SRA741696	Gov of Canada	Gov of Canada	1	0.94238	0.09347	0.76404	0.51048	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48979	48979	SRR7535437	SRX4403221	SRS3557710	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample33	F3LFL4	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3LFL4 L33	F3LFL4 L33	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3LFL4.fastq.gz	fastq	3167171318.0	37581804.0	F3LFL4.fastq.gz	0:84.27 1:0	A:836474638;C:736638892;G:687417511;T:906580806;N:59471	84	0	836474638	736638892	687417511	906580806	59471	SRX4403221	SRS3557710	SRA741696	Gov of Canada	Gov of Canada	1	0.95381	0.0776	0.74432	0.49786	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48980	48980	SRR7535438	SRX4403220	SRS3557709	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample32	F3LFL3	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3LFL3 L32	F3LFL3 L32	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3LFL3.fastq.gz	fastq	3969872568.0	47103172.0	F3LFL3.fastq.gz	0:84.28 1:0	A:1087899347;C:891968649;G:846315646;T:1143611603;N:77323	84	0	1087899347	891968649	846315646	1143611603	77323	SRX4403220	SRS3557709	SRA741696	Gov of Canada	Gov of Canada	1	0.94717	0.08461	0.74714	0.53355	84	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48981	48981	SRR7535439	SRX4403219	SRS3557708	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample31	F3LFL2	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3LFL2 L31	F3LFL2 L31	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3LFL2.fastq.gz	fastq	2401613544.0	31959346.0	F3LFL2.fastq.gz	0:75.15 1:0	A:673230842;C:536445759;G:492980009;T:698882870;N:74064	75	0	673230842	536445759	492980009	698882870	74064	SRX4403219	SRS3557708	SRA741696	Gov of Canada	Gov of Canada	1	0.95198	0.08486	0.7878	0.55398	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48982	48982	SRR7535440	SRX4403218	SRS3557706	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample40	F3HFL3	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3HFL3 L40	F3HFL3 L40	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3HFL3.fastq.gz	fastq	2266960447.0	26913177.0	F3HFL3.fastq.gz	0:84.23 1:0	A:590021990;C:520283209;G:479594101;T:677024566;N:36581	84	0	590021990	520283209	479594101	677024566	36581	SRX4403218	SRS3557706	SRA741696	Gov of Canada	Gov of Canada	1	0.94897	0.08251	0.80848	0.57355	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
48983	48983	SRR7535441	SRX4403217	SRS3557707	SRP154295	PRJNA481502	Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio	PRJNA481502	Transcriptome Analysis	Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.		pubmed:30530669	sample39	F3HFL2	strain:AB strain\|age:6 mpf organism or animal									RNA seq of Danio rerio: male kidney	F3HFL2 L39	F3HFL2 L39	mRNA seq from total RNA on Illumina Neoprep			RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500	SRP154295		F3HFL2.fastq.gz	fastq	2749128323.0	32649931.0	F3HFL2.fastq.gz	0:84.20 1:0	A:739282939;C:602311637;G:590565979;T:816929591;N:38177	84	0	739282939	602311637	590565979	816929591	38177	SRX4403217	SRS3557707	SRA741696	Gov of Canada	Gov of Canada	1	0.9613	0.09046	0.8104	0.62158	85	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Canada	2018-12-11	Adult	Adult	Kidney	Renal System
49049	49049	SRR7633485	SRX4497216	SRS3618216	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233	G2 pod 03	GSM3317057	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G2 mRNA	G2 pod 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G2 mRNA	GSM3317057	GSM3317057: G2 pod 03; Danio rerio; RNA Seq	GSM3317057		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317057	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S9_trimmed.fastq.gz	fastq	1265733350.0	25073196.0	GSM3317057 r1	0:50.48 1:0	A:351449147;C:285891495;G:278677300;T:349486454;N:228954	50	0	351449147	285891495	278677300	349486454	228954	SRX4497216	SRS3618216	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.88664	0.09978	0.70747	0.46307	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49050	49050	SRR7633484	SRX4497215	SRS3618215	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233	G2 pod 02	GSM3317056	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G2 mRNA	G2 pod 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G2 mRNA	GSM3317056	GSM3317056: G2 pod 02; Danio rerio; RNA Seq	GSM3317056		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317056	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S8_trimmed.fastq.gz	fastq	927703036.0	18397661.0	GSM3317056 r1	0:50.43 1:0	A:256098583;C:212027468;G:205646180;T:253765375;N:165430	50	0	256098583	212027468	205646180	253765375	165430	SRX4497215	SRS3618215	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.82269	0.09332	0.70676	0.47673	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49051	49051	SRR7633483	SRX4497214	SRS3618214	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233	G2 pod 01	GSM3317055	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G2 mRNA	G2 pod 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G2 mRNA	GSM3317055	GSM3317055: G2 pod 01; Danio rerio; RNA Seq	GSM3317055		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317055	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S7_trimmed.fastq.gz	fastq	1868917850.0	36965227.0	GSM3317055 r1	0:50.56 1:0	A:518334465;C:423085551;G:412301170;T:514857394;N:339270	50	0	518334465	423085551	412301170	514857394	339270	SRX4497214	SRS3618214	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.8967	0.11444	0.66793	0.47524	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49052	49052	SRR7633482	SRX4497213	SRS3618213	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233	G0 pod 03	GSM3317054	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G0 mRNA	G0 pod 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G0 mRNA	GSM3317054	GSM3317054: G0 pod 03; Danio rerio; RNA Seq	GSM3317054		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317054	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S6_trimmed.fastq.gz	fastq	1989842108.0	39354652.0	GSM3317054 r1	0:50.56 1:0	A:547820589;C:452831323;G:441782569;T:547047192;N:360435	50	0	547820589	452831323	441782569	547047192	360435	SRX4497213	SRS3618213	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.88797	0.1001	0.67016	0.46755	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49053	49053	SRR7633481	SRX4497212	SRS3618212	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233	G0 pod 02	GSM3317053	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G0 mRNA	G0 pod 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G0 mRNA	GSM3317053	GSM3317053: G0 pod 02; Danio rerio; RNA Seq	GSM3317053		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317053	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S5_trimmed.fastq.gz	fastq	1784099065.0	35295758.0	GSM3317053 r1	0:50.55 1:0	A:493338451;C:401706697;G:388876128;T:499853218;N:324571	50	0	493338451	401706697	388876128	499853218	324571	SRX4497212	SRS3618212	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.86757	0.09319	0.6733	0.46511	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49054	49054	SRR7633480	SRX4497211	SRS3618211	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233	G0 pod 01	GSM3317052	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G0 mRNA	G0 pod 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G0 mRNA	GSM3317052	GSM3317052: G0 pod 01; Danio rerio; RNA Seq	GSM3317052		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317052	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S4_trimmed.fastq.gz	fastq	1294942611.0	25649695.0	GSM3317052 r1	0:50.49 1:0	A:358939215;C:292943376;G:284204779;T:358621256;N:233985	50	0	358939215	292943376	284204779	358621256	233985	SRX4497211	SRS3618211	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89677	0.09742	0.66695	0.46036	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49055	49055	SRR7633479	SRX4497210	SRS3618210	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233	control pod 03	GSM3317051	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:control	control pod 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:control	GSM3317051	GSM3317051: control pod 03; Danio rerio; RNA Seq	GSM3317051		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317051	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S3_trimmed.fastq.gz	fastq	1864996530.0	36896407.0	GSM3317051 r1	0:50.55 1:0	A:514542102;C:423583183;G:412707586;T:513826127;N:337532	50	0	514542102	423583183	412707586	513826127	337532	SRX4497210	SRS3618210	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89167	0.10091	0.67773	0.48093	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49056	49056	SRR7633478	SRX4497209	SRS3618209	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233	control pod 02	GSM3317050	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:control	control pod 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:control	GSM3317050	GSM3317050: control pod 02; Danio rerio; RNA Seq	GSM3317050		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317050	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S2_trimmed.fastq.gz	fastq	1405360276.0	27811908.0	GSM3317050 r1	0:50.53 1:0	A:388467227;C:319138771;G:310773160;T:386727396;N:253722	50	0	388467227	319138771	310773160	386727396	253722	SRX4497209	SRS3618209	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.898	0.10269	0.66967	0.45546	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49057	49057	SRR7633477	SRX4497208	SRS3618208	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233	control pod 01	GSM3317049	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:control	control pod 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:control	GSM3317049	GSM3317049: control pod 01; Danio rerio; RNA Seq	GSM3317049		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317049	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S1_trimmed.fastq.gz	fastq	931525657.0	18454172.0	GSM3317049 r1	0:50.48 1:0	A:259125695;C:210068089;G:204402139;T:257763012;N:166722	50	0	259125695	210068089	204402139	257763012	166722	SRX4497208	SRS3618208	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89072	0.10423	0.67107	0.46057	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
51852	51852	SRR10358701	SRX7068102	SRS5584514	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.			Model organism or animal sample from Danio rerio	miRNA WT SVCV	strain:Wild type\|age:6 month\|sex:pooled male and female\|tissue:kidney\|BioSampleModel:Model organism or animal									miRNA WT SVCV	miRNA WT SVCV	miRNA WT SVCV	Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.			miRNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP192333		WT-SVCV_1.fastq.gz	fastq	1316699181.0	25817631.0	WT SVCV 1.fastq.gz	0:51	A:276414308;C:338128957;G:380963712;T:321185951;N:6253	51		276414308	338128957	380963712	321185951	6253	SRX7068102	SRS5584514	SRA986546	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	1	0.12679	0.0134	0.9931	0.63608	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	Spain	2019-10-29	Adult	Adult	Kidney	Renal System
51853	51853	SRR10358540	SRX7067941	SRS5584353	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.			Model organism or animal sample from Danio rerio	miRNA WT Control	strain:Wild type\|age:6 month\|sex:pooled male and female\|tissue:kidney\|BioSampleModel:Model organism or animal									miRNA WT Control	miRNA WT Control	miRNA WT Control	Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.			miRNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP192333		WT-C_1.fastq.gz	fastq	1391330184.0	27280984.0	WT C 1.fastq.gz	0:51	A:252097427;C:365291036;G:426841004;T:347094254;N:6463	51		252097427	365291036	426841004	347094254	6463	SRX7067941	SRS5584353	SRA986495	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	1	0.01783	0.00242	0.99411	0.61368	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	Spain	2019-10-29	Adult	Adult	Kidney	Renal System
59301	59301	SRR11851897	SRX8402007	SRS6714764	SRP264841	PRJNA635161	Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]	GSE151231	Transcriptome Analysis	Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.	parent bioproject:PRJNA635158	pubmed:34170284	scRNA seq gata2b ko 3	GSM4568915	tissue:sorted marrow cells\|cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b ko	scRNA seq gata2b ko 3	The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds	sorted marrow cells	Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	Freshly isolated kidney marrow cells from euthanized adult zebrafish.	cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b ko	GSM4568915	GSM4568915: scRNA seq gata2b ko 3; Danio rerio; RNA Seq	GSM4568915		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	GEO Accession:GSM4568915	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP264841	loader:fastq load.py\|options: appendBCtoName	KO3_Single_Cell_GAGACGGA.fastq.sorted.fastq.gz	fastq	3768784245.0	63353331.0	GSM4568915 r1	0:59.49	A:1049235928;C:815061845;G:790664763;T:1113812557;N:9152	59		1049235928	815061845	790664763	1113812557	9152	SRX8402007	SRS6714764	SRA1080050	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.9009	0.07395	0.83524	0.54215	60	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2020-05-26	Adult	Adult	Marrow	Renal System
59302	59302	SRR11851896	SRX8402006	SRS6714763	SRP264841	PRJNA635161	Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]	GSE151231	Transcriptome Analysis	Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.	parent bioproject:PRJNA635158	pubmed:34170284	scRNA seq gata2b ko 2	GSM4568914	tissue:sorted marrow cells\|cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b ko	scRNA seq gata2b ko 2	The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds	sorted marrow cells	Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	Freshly isolated kidney marrow cells from euthanized adult zebrafish.	cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b ko	GSM4568914	GSM4568914: scRNA seq gata2b ko 2; Danio rerio; RNA Seq	GSM4568914		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	GEO Accession:GSM4568914	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP264841	loader:fastq load.py\|options: appendBCtoName	KO2_Single_Cell_TTACCTCC.fastq.sorted.fastq.gz	fastq	5788926123.0	96793878.0	GSM4568914 r1	0:59.81	A:1591846184;C:1284226924;G:1217400432;T:1695437315;N:15268	59		1591846184	1284226924	1217400432	1695437315	15268	SRX8402006	SRS6714763	SRA1080050	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.90311	0.0768	0.82227	0.56806	61	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2020-05-26	Adult	Adult	Marrow	Renal System
59303	59303	SRR11851895	SRX8402005	SRS6714762	SRP264841	PRJNA635161	Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]	GSE151231	Transcriptome Analysis	Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.	parent bioproject:PRJNA635158	pubmed:34170284	scRNA seq gata2b ko 1	GSM4568913	tissue:sorted marrow cells\|cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b ko	scRNA seq gata2b ko 1	The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds	sorted marrow cells	Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	Freshly isolated kidney marrow cells from euthanized adult zebrafish.	cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b ko	GSM4568913	GSM4568913: scRNA seq gata2b ko 1; Danio rerio; RNA Seq	GSM4568913		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	GEO Accession:GSM4568913	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP264841	loader:fastq load.py\|options: appendBCtoName	KO1_Single_Cell_TAAGGCTC.fastq.sorted.fastq.gz	fastq	4485434923.0	75329131.0	GSM4568913 r1	0:59.54	A:1245571394;C:1005814804;G:944318855;T:1289711080;N:18790	59		1245571394	1005814804	944318855	1289711080	18790	SRX8402005	SRS6714762	SRA1080050	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.89937	0.06305	0.83879	0.54954	61	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2020-05-26	Adult	Adult	Marrow	Renal System
59304	59304	SRR11851894	SRX8402004	SRS6714761	SRP264841	PRJNA635161	Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]	GSE151231	Transcriptome Analysis	Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.	parent bioproject:PRJNA635158	pubmed:34170284	scRNA seq gata2b het 3	GSM4568912	tissue:sorted marrow cells\|cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b het	scRNA seq gata2b het 3	The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds	sorted marrow cells	Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	Freshly isolated kidney marrow cells from euthanized adult zebrafish.	cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b het	GSM4568912	GSM4568912: scRNA seq gata2b het 3; Danio rerio; RNA Seq	GSM4568912		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	GEO Accession:GSM4568912	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP264841	loader:fastq load.py\|options: appendBCtoName	HET3_Single_Cell_CCTTTACT.fastq.sorted.fastq.gz	fastq	3696586389.0	62109708.0	GSM4568912 r1	0:59.52	A:1054965741;C:827475497;G:744430159;T:1069699165;N:15827	59		1054965741	827475497	744430159	1069699165	15827	SRX8402004	SRS6714761	SRA1080050	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.89246	0.06392	0.83934	0.56422	58	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2020-05-26	Adult	Adult	Marrow	Renal System
59305	59305	SRR11851893	SRX8402003	SRS6714760	SRP264841	PRJNA635161	Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]	GSE151231	Transcriptome Analysis	Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.	parent bioproject:PRJNA635158	pubmed:34170284	scRNA seq gata2b het 2	GSM4568911	tissue:sorted marrow cells\|cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b het	scRNA seq gata2b het 2	The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds	sorted marrow cells	Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	Freshly isolated kidney marrow cells from euthanized adult zebrafish.	cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b het	GSM4568911	GSM4568911: scRNA seq gata2b het 2; Danio rerio; RNA Seq	GSM4568911		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	GEO Accession:GSM4568911	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP264841	loader:fastq load.py\|options: appendBCtoName	HET2_Single_Cell_CAGTTATG.fastq.sorted.fastq.gz	fastq	5357974983.0	89558550.0	GSM4568911 r1	0:59.83	A:1490260317;C:1191725100;G:1122517464;T:1553457613;N:14489	59		1490260317	1191725100	1122517464	1553457613	14489	SRX8402003	SRS6714760	SRA1080050	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.90302	0.07865	0.82603	0.57406	61	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2020-05-26	Adult	Adult	Marrow	Renal System
59306	59306	SRR11851892	SRX8402002	SRS6714759	SRP264841	PRJNA635161	Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]	GSE151231	Transcriptome Analysis	Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.	parent bioproject:PRJNA635158	pubmed:34170284	scRNA seq gata2b het 1	GSM4568910	tissue:sorted marrow cells\|cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b het	scRNA seq gata2b het 1	The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds	sorted marrow cells	Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	Freshly isolated kidney marrow cells from euthanized adult zebrafish.	cell type:sorted marrow cells\|age:4 mpf\|genotype:gata2b het	GSM4568910	GSM4568910: scRNA seq gata2b het 1; Danio rerio; RNA Seq	GSM4568910		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	GEO Accession:GSM4568910	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP264841	loader:fastq load.py\|options: appendBCtoName	HET1_Single_Cell_ATAGCCTT.fastq.sorted.fastq.gz	fastq	4701831804.0	78923769.0	GSM4568910 r1	0:59.57	A:1307674780;C:1043797904;G:1001646002;T:1348693620;N:19498	59		1307674780	1043797904	1001646002	1348693620	19498	SRX8402002	SRS6714759	SRA1080050	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.90603	0.07667	0.82704	0.57543	61	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2020-05-26	Adult	Adult	Marrow	Renal System
59307	59307	SRR11851891	SRX8402001	SRS6714758	SRP264841	PRJNA635161	Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]	GSE151231	Transcriptome Analysis	Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.	parent bioproject:PRJNA635158	pubmed:34170284	scRNA seq wildtype 3	GSM4568909	tissue:sorted marrow cells\|cell type:sorted marrow cells\|age:4 mpf\|genotype:wildtype	scRNA seq wildtype 3	The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds	sorted marrow cells	Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	Freshly isolated kidney marrow cells from euthanized adult zebrafish.	cell type:sorted marrow cells\|age:4 mpf\|genotype:wildtype	GSM4568909	GSM4568909: scRNA seq wildtype 3; Danio rerio; RNA Seq	GSM4568909		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	GEO Accession:GSM4568909	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP264841	loader:fastq load.py\|options: appendBCtoName	WT3_Single_Cell_AGAAAGCT.fastq.sorted.fastq.gz	fastq	3348785686.0	56255768.0	GSM4568909 r1	0:59.53	A:955572407;C:728586737;G:678902164;T:985710022;N:14356	59		955572407	728586737	678902164	985710022	14356	SRX8402001	SRS6714758	SRA1080050	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.88271	0.06967	0.8284	0.54728	61	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2020-05-26	Adult	Adult	Marrow	Renal System
59308	59308	SRR11851890	SRX8402000	SRS6714757	SRP264841	PRJNA635161	Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]	GSE151231	Transcriptome Analysis	Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.	parent bioproject:PRJNA635158	pubmed:34170284	scRNA seq wildtype 2	GSM4568908	tissue:sorted marrow cells\|cell type:sorted marrow cells\|age:4 mpf\|genotype:wildtype	scRNA seq wildtype 2	The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds	sorted marrow cells	Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	Freshly isolated kidney marrow cells from euthanized adult zebrafish.	cell type:sorted marrow cells\|age:4 mpf\|genotype:wildtype	GSM4568908	GSM4568908: scRNA seq wildtype 2; Danio rerio; RNA Seq	GSM4568908		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	GEO Accession:GSM4568908	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP264841	loader:fastq load.py\|options: appendBCtoName	WT2_Single_Cell_TCGCATAA.fastq.sorted.fastq.gz	fastq	3812899254.0	63738225.0	GSM4568908 r1	0:59.82	A:1040969741;C:863166087;G:810647668;T:1098105772;N:9986	59		1040969741	863166087	810647668	1098105772	9986	SRX8402000	SRS6714757	SRA1080050	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.91023	0.06938	0.83238	0.54799	59	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2020-05-26	Adult	Adult	Marrow	Renal System
59309	59309	SRR11851889	SRX8401999	SRS6714756	SRP264841	PRJNA635161	Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]	GSE151231	Transcriptome Analysis	Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.	parent bioproject:PRJNA635158	pubmed:34170284	scRNA seq wildtype 1	GSM4568907	tissue:sorted marrow cells\|cell type:sorted marrow cells\|age:4 mpf\|genotype:wildtype	scRNA seq wildtype 1	The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds	sorted marrow cells	Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	Freshly isolated kidney marrow cells from euthanized adult zebrafish.	cell type:sorted marrow cells\|age:4 mpf\|genotype:wildtype	GSM4568907	GSM4568907: scRNA seq wildtype 1; Danio rerio; RNA Seq	GSM4568907		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops	GEO Accession:GSM4568907	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP264841	loader:fastq load.py\|options: appendBCtoName	WT1_Single_Cell_CTTAATAG.fastq.sorted.fastq.gz	fastq	3675748091.0	61731984.0	GSM4568907 r1	0:59.54	A:1040800033;C:822608649;G:765542043;T:1046781383;N:15983	59		1040800033	822608649	765542043	1046781383	15983	SRX8401999	SRS6714756	SRA1080050	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.8978	0.05341	0.84167	0.59389	61	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2020-05-26	Adult	Adult	Marrow	Renal 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");;