metadata: run_metadata: 108 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and tissue_curation

108 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" 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.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
34960	34960	SRR32588717	SRX27895234	SRS24266236	SRP568323	PRJNA1232602	Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains	PRJNA1232602	Other	In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.			Iso Seq RNA from Danio rerio	C2 F2 F K	strain:NHGRI2\|isolate:Single paired cross\|breed:Zebrafish\|cultivar:wild type\|ecotype:United States\|age:9 month\|dev stage:adult fish\|collection date:2024 06\|geo loc name:USA\|sex:female\|tissue:kidney\|BioSampleModel:Model organism or animal									Iso Seq RNA from kidney	C2 F2 F K	C2 F2 F K	The long Read Sequencing libraries was sequenced using PacBio Sequel II			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	PACBIO_SMRT	Sequel II	SRP568323		m84270_240904_132604_s1.skera.flnc.fastq.gz	fastq	109258150145.0	61126158.0	m84270 240904 132604 s1.skera.flnc.fastq.gz	0:1787.42	A:32153042096;C:22604112467;G:23394852841;T:31106142741;N:0	1787		32153042096	22604112467	23394852841	31106142741	0	SRX27895234	SRS24266236	SRA2089085	National Human Genome Research Institute\|Translational and Functional Genomics Branch	National Human Genome Research Institute National Human Genome Research Institute												T		long read	pacbio	pacbio_modern	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2025-03-06	Adult	Adult	Kidney	Renal System
34970	34970	SRR32588727	SRX27895224	SRS24266224	SRP568323	PRJNA1232602	Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains	PRJNA1232602	Other	In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.			Iso Seq RNA from Danio rerio	C2 F2 M K22	strain:NHGRI2\|isolate:Single paired cross\|breed:Zebrafish\|cultivar:wild type\|ecotype:United States\|age:9 month\|dev stage:adult fish\|collection date:2024 06\|geo loc name:USA\|sex:male\|tissue:kidney\|BioSampleModel:Model organism or animal									Iso Seq RNA from kidney	C2 F2 M K22	C2 F2 M K22	The long Read Sequencing libraries was sequenced using PacBio Sequel II			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	PACBIO_SMRT	Sequel II	SRP568323		m64467e_240829_144745.hifi_reads.flnc.fastq.gz	fastq	14838539048.0	3383142.0	m64467e 240829 144745.hifi reads.flnc.fastq.gz	0:4386.02	A:4211191682;C:3185079857;G:3320422646;T:4121844863;N:0	4386		4211191682	3185079857	3320422646	4121844863	0	SRX27895224	SRS24266224	SRA2089085	National Human Genome Research Institute\|Translational and Functional Genomics Branch	National Human Genome Research Institute National Human Genome Research Institute												T		long read	pacbio	pacbio_modern	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2025-03-06	Adult	Adult	Kidney	Renal System
34971	34971	SRR32588728	SRX27895223	SRS24266234	SRP568323	PRJNA1232602	Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains	PRJNA1232602	Other	In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.			Iso Seq RNA from Danio rerio	C2 F2 M K21	strain:NHGRI2\|isolate:Single paired cross\|breed:Zebrafish\|cultivar:wild type\|ecotype:United States\|age:9 month\|dev stage:adult fish\|collection date:2024 06\|geo loc name:USA\|sex:male\|tissue:Kidney\|BioSampleModel:Model organism or animal									Iso Seq RNA from kidney	C2 F2 M K21	C2 F2 M K21	The long Read Sequencing libraries was sequenced using PacBio Sequel II			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	PACBIO_SMRT	Sequel II	SRP568323		m84270_240913_170640_s3.skera.flnc.fastq.gz	fastq	100849133955.0	51593887.0	m84270 240913 170640 s3.skera.flnc.fastq.gz	0:1954.67	A:28887816631;C:21568633305;G:22323254809;T:28069429210;N:0	1954		28887816631	21568633305	22323254809	28069429210	0	SRX27895223	SRS24266234	SRA2089085	National Human Genome Research Institute\|Translational and Functional Genomics Branch	National Human Genome Research Institute National Human Genome Research Institute												T		long read	pacbio	pacbio_modern	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2025-03-06	Adult	Adult	Kidney	Renal System
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
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
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
60502	60502	SRR12338629	SRX8838545	SRS7101853	SRP273930	PRJNA649208	A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation	GSE155258	Transcriptome Analysis	Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …			AMut3 S16	GSM4698247	source name:grna / mutant fish\|tissue:kidney marrow\|genotype:grna /	AMut3 S16	RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.	grna / mutant fish	Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.	tissue:kidney marrow\|genotype:grna /	GSM4698247	GSM4698247: AMut3 S16; Danio rerio; RNA Seq	GSM4698247		1	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	GEO Accession:GSM4698247	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP273930		AMut3_S16_L003_R1_001.fastq.gz	fastq	1660975744.0	21854944.0	GSM4698247 r1	0:76 1:0	A:403133854;C:408666497;G:390547168;T:458402036;N:226189	76	0	403133854	408666497	390547168	458402036	226189	SRX8838545	SRS7101853	SRA1104643	GEO	Boolean, Pediatrics, UCSD	1	0.88856		0.071		0.7331		0.50274		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2020-07-28	Undetermined	Undetermined	Kidney	Renal System
60503	60503	SRR12338628	SRX8838544	SRS7101852	SRP273930	PRJNA649208	A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation	GSE155258	Transcriptome Analysis	Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …			AMut2 S15	GSM4698246	source name:grna / mutant fish\|tissue:kidney marrow\|genotype:grna /	AMut2 S15	RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.	grna / mutant fish	Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.	tissue:kidney marrow\|genotype:grna /	GSM4698246	GSM4698246: AMut2 S15; Danio rerio; RNA Seq	GSM4698246		1	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	GEO Accession:GSM4698246	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP273930		AMut2_S15_L003_R1_001.fastq.gz	fastq	1932204620.0	25423745.0	GSM4698246 r1	0:76 1:0	A:471753150;C:472824626;G:455434892;T:531926834;N:265118	76	0	471753150	472824626	455434892	531926834	265118	SRX8838544	SRS7101852	SRA1104643	GEO	Boolean, Pediatrics, UCSD	1	0.88563		0.0647		0.73054		0.51301		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2020-07-28	Undetermined	Undetermined	Kidney	Renal System
60504	60504	SRR12338627	SRX8838543	SRS7101851	SRP273930	PRJNA649208	A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation	GSE155258	Transcriptome Analysis	Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …			AMut1 S14	GSM4698245	source name:grna / mutant fish\|tissue:kidney marrow\|genotype:grna /	AMut1 S14	RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.	grna / mutant fish	Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.	tissue:kidney marrow\|genotype:grna /	GSM4698245	GSM4698245: AMut1 S14; Danio rerio; RNA Seq	GSM4698245		1	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	GEO Accession:GSM4698245	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP273930		AMut1_S14_L003_R1_001.fastq.gz	fastq	1576218644.0	20739719.0	GSM4698245 r1	0:76 1:0	A:382135276;C:389342906;G:367829537;T:436699819;N:211106	76	0	382135276	389342906	367829537	436699819	211106	SRX8838543	SRS7101851	SRA1104643	GEO	Boolean, Pediatrics, UCSD	1	0.88823		0.07406		0.73062		0.50537		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2020-07-28	Undetermined	Undetermined	Kidney	Renal System
60505	60505	SRR12338626	SRX8838542	SRS7101850	SRP273930	PRJNA649208	A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation	GSE155258	Transcriptome Analysis	Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …			WT3 S13	GSM4698244	source name:grna+/+ control fish\|tissue:kidney marrow\|genotype:WT	WT3 S13	RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.	grna+/+ control fish	Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.	tissue:kidney marrow\|genotype:WT	GSM4698244	GSM4698244: WT3 S13; Danio rerio; RNA Seq	GSM4698244		1	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	GEO Accession:GSM4698244	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP273930		WT3_S13_L003_R1_001.fastq.gz	fastq	1763410824.0	23202774.0	GSM4698244 r1	0:76 1:0	A:423301555;C:439721210;G:408339976;T:491805474;N:242609	76	0	423301555	439721210	408339976	491805474	242609	SRX8838542	SRS7101850	SRA1104643	GEO	Boolean, Pediatrics, UCSD	1	0.89892		0.06886		0.74408		0.49795		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2020-07-28	Undetermined	Undetermined	Kidney	Renal System
60506	60506	SRR12338625	SRX8838541	SRS7101849	SRP273930	PRJNA649208	A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation	GSE155258	Transcriptome Analysis	Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …			WT2 S12	GSM4698243	source name:grna+/+ control fish\|tissue:kidney marrow\|genotype:WT	WT2 S12	RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.	grna+/+ control fish	Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.	tissue:kidney marrow\|genotype:WT	GSM4698243	GSM4698243: WT2 S12; Danio rerio; RNA Seq	GSM4698243		1	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	GEO Accession:GSM4698243	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP273930		WT2_S12_L003_R1_001.fastq.gz	fastq	1637691700.0	21548575.0	GSM4698243 r1	0:76 1:0	A:405974612;C:400305204;G:377359541;T:453830617;N:221726	76	0	405974612	400305204	377359541	453830617	221726	SRX8838541	SRS7101849	SRA1104643	GEO	Boolean, Pediatrics, UCSD	1	0.89995		0.07959		0.7429		0.5021		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2020-07-28	Undetermined	Undetermined	Kidney	Renal System
60507	60507	SRR12338624	SRX8838540	SRS7101848	SRP273930	PRJNA649208	A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation	GSE155258	Transcriptome Analysis	Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …			WT1 S11	GSM4698242	source name:grna+/+ control fish\|tissue:kidney marrow\|genotype:WT	WT1 S11	RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.	grna+/+ control fish	Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.	tissue:kidney marrow\|genotype:WT	GSM4698242	GSM4698242: WT1 S11; Danio rerio; RNA Seq	GSM4698242		1	Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.	GEO Accession:GSM4698242	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP273930		WT1_S11_L003_R1_001.fastq.gz	fastq	1817974948.0	23920723.0	GSM4698242 r1	0:76 1:0	A:445440119;C:445993982;G:423050638;T:503235344;N:254865	76	0	445440119	445993982	423050638	503235344	254865	SRX8838540	SRS7101848	SRA1104643	GEO	Boolean, Pediatrics, UCSD	1	0.89811		0.07554		0.72908		0.4892		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2020-07-28	Undetermined	Undetermined	Kidney	Renal System
60908	60908	SRR12654012	SRX9135234	SRS7377188	SRP282618	PRJNA663897	Identification of enhancer elements that direct long range responses to tissue injury	GSE158079	Other	The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain post cardiac injury. Overall design: Brain and kidney RNA seq and ATAC seq profiling post cardiac injury; cebpd+/+ and cebpd / brain RNA seq profiling post cardiac injury		pubmed:35513710	WKM RNAseq uninjured rep2	GSM4790351	source name:Whole kidney marrow\|strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:uninjured	WKM RNAseq uninjured rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	Whole kidney marrow	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:uninjured	GSM4790351	GSM4790351: WKM RNAseq uninjured rep2; Danio rerio; RNA Seq	GSM4790351		1	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	GEO Accession:GSM4790351	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP282618		WKM.RNAseq.Uninjured.S6_S17_L007_R1_001.fastq.gz	fastq	2128727352.0	41739752.0	GSM4790351 r1	0:51 1:0	A:526003466;C:520045952;G:479756780;T:602686415;N:234739	51	0	526003466	520045952	479756780	602686415	234739	SRX9135234	SRS7377188	SRA1126400	GEO	Poss, Cell Biology, Duke University	1	0.91364		0.16098		0.72101		0.55063		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-09-16	Larval	Larval	Kidney	Renal System
60909	60909	SRR12654011	SRX9135233	SRS7377187	SRP282618	PRJNA663897	Identification of enhancer elements that direct long range responses to tissue injury	GSE158079	Other	The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain post cardiac injury. Overall design: Brain and kidney RNA seq and ATAC seq profiling post cardiac injury; cebpd+/+ and cebpd / brain RNA seq profiling post cardiac injury		pubmed:35513710	WKM RNAseq uninjured rep1	GSM4790350	source name:Whole kidney marrow\|strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:uninjured	WKM RNAseq uninjured rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	Whole kidney marrow	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:uninjured	GSM4790350	GSM4790350: WKM RNAseq uninjured rep1; Danio rerio; RNA Seq	GSM4790350		1	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	GEO Accession:GSM4790350	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP282618		WKM.RNAseq.Uninjured.S4_S16_L007_R1_001.fastq.gz	fastq	2227157658.0	43669758.0	GSM4790350 r1	0:51 1:0	A:537108530;C:560518473;G:511205641;T:618080406;N:244608	51	0	537108530	560518473	511205641	618080406	244608	SRX9135233	SRS7377187	SRA1126400	GEO	Poss, Cell Biology, Duke University	1	0.92052		0.16555		0.72206		0.54742		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-09-16	Larval	Larval	Kidney	Renal System
60910	60910	SRR12654010	SRX9135232	SRS7377186	SRP282618	PRJNA663897	Identification of enhancer elements that direct long range responses to tissue injury	GSE158079	Other	The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain post cardiac injury. Overall design: Brain and kidney RNA seq and ATAC seq profiling post cardiac injury; cebpd+/+ and cebpd / brain RNA seq profiling post cardiac injury		pubmed:35513710	WKM RNAseq regeneration rep2	GSM4790349	source name:Whole kidney marrow\|strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:cardiomyocyte ablation	WKM RNAseq regeneration rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	Whole kidney marrow	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM4790349	GSM4790349: WKM RNAseq regeneration rep2; Danio rerio; RNA Seq	GSM4790349		1	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	GEO Accession:GSM4790349	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP282618		WKM.RNAseq.Injured.S3_S15_L007_R1_001.fastq.gz	fastq	2221210599.0	43553149.0	GSM4790349 r1	0:51 1:0	A:550217634;C:538023788;G:499202852;T:633520371;N:245954	51	0	550217634	538023788	499202852	633520371	245954	SRX9135232	SRS7377186	SRA1126400	GEO	Poss, Cell Biology, Duke University	1	0.91459		0.14893		0.7152		0.53335		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-09-16	Larval	Larval	Kidney	Renal System
60911	60911	SRR12654009	SRX9135231	SRS7377185	SRP282618	PRJNA663897	Identification of enhancer elements that direct long range responses to tissue injury	GSE158079	Other	The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain post cardiac injury. Overall design: Brain and kidney RNA seq and ATAC seq profiling post cardiac injury; cebpd+/+ and cebpd / brain RNA seq profiling post cardiac injury		pubmed:35513710	WKM RNAseq regeneration rep1	GSM4790348	source name:Whole kidney marrow\|strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:cardiomyocyte ablation	WKM RNAseq regeneration rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	Whole kidney marrow	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM4790348	GSM4790348: WKM RNAseq regeneration rep1; Danio rerio; RNA Seq	GSM4790348		1	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	GEO Accession:GSM4790348	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP282618		WKM.RNAseq.Injured.S1_S14_L007_R1_001.fastq.gz	fastq	1732396917.0	33968567.0	GSM4790348 r1	0:51 1:0	A:421512333;C:432906390;G:394818884;T:482970998;N:188312	51	0	421512333	432906390	394818884	482970998	188312	SRX9135231	SRS7377185	SRA1126400	GEO	Poss, Cell Biology, Duke University	1	0.91203		0.15222		0.71486		0.54145		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-09-16	Larval	Larval	Kidney	Renal System
69454	69454	SRR21377195	SRX17382862	SRS14941934	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.			7d chd8 / zebrafish rep3	GSM6532689	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf /	7d chd8 / zebrafish rep3	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	40 chd8 / zebrafish embryos at 5 dpf were collected and anesthetized in 0.4% 4g/L tricane. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h. The intestines were removed and collected by tweezers under the microscope and the isolated tissue was then transfered into Trizol. About 70 chd8 / zebrafish embryos at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane. Then the media were replaced with RNAlater RNA Solution and samples were storaged at 4℃ for more than 24h. Their kidneys were removed by tweezers under the microscope. Then the tissues were immersed in Trizol and the RNA of them were extracted as previously described for intestine tissues.	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with fish feeding circulation system water and allowed to mate for no more than 1 hour. Fertilized eggs were transfered into petri dishes less than 100 embryos per dish with embryo media. Then all of the embryos are incubated at 28.5℃ until the 5 dpf or 7 dpf. Embryo media:1L ddH2O with 10 ml stock solution A 1 mL stock solution B 10 mL stock solution C 10 mL stock solution D and 10 mL stock solution E adjust pH to 7.2 with 1 M HCl.A: 250 mL RO H2O 20 g NaCl 1 g KCl;B: 100 mL RO H2O 0.358 g Na2HPO4 anhydrous 0.6 g KH2PO4 monobasic;C: 250 mL RO H2O 4.68 g CaCl2 dihydrate;D: 250 mL RO H2O 6.15 g MgSO4·7H2O;E: 250 mL RO H2O 8.75 g NaHCO3. System water:purified water with sea salt and NaHCO3，conductivity 450 500 μs/cm，pH 7.0±0.2.	strain:AB\|tissue:kidney\|age:7 dpf /	GSM6532689	GSM6532689: 7d chd8 / zebrafish rep3; Danio rerio; RNA Seq	GSM6532689 r1	GSM6532689	1	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_chd8_3.fq.gz	fastq	5703645600.0	19012152.0	GSM6532689 r1	0:150 1:150	A:1472893141;C:1378744688;G:1384835454;T:1466499737;N:672580	150	150	1472893141	1378744688	1384835454	1466499737	672580	SRX17382862	SRS14941934			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.96656	0.96614	0.06713	0.06541	0.71451	0.71713	0.47578	0.47388	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-08-31	Larval	Larval	Kidney	Renal System
69455	69455	SRR21377196	SRX17382861	SRS14941973	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.			7d chd8 / zebrafish rep2	GSM6532688	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf /	7d chd8 / zebrafish rep2	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	40 chd8 / zebrafish embryos at 5 dpf were collected and anesthetized in 0.4% 4g/L tricane. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h. The intestines were removed and collected by tweezers under the microscope and the isolated tissue was then transfered into Trizol. About 70 chd8 / zebrafish embryos at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane. Then the media were replaced with RNAlater RNA Solution and samples were storaged at 4℃ for more than 24h. Their kidneys were removed by tweezers under the microscope. Then the tissues were immersed in Trizol and the RNA of them were extracted as previously described for intestine tissues.	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with fish feeding circulation system water and allowed to mate for no more than 1 hour. Fertilized eggs were transfered into petri dishes less than 100 embryos per dish with embryo media. Then all of the embryos are incubated at 28.5℃ until the 5 dpf or 7 dpf. Embryo media:1L ddH2O with 10 ml stock solution A 1 mL stock solution B 10 mL stock solution C 10 mL stock solution D and 10 mL stock solution E adjust pH to 7.2 with 1 M HCl.A: 250 mL RO H2O 20 g NaCl 1 g KCl;B: 100 mL RO H2O 0.358 g Na2HPO4 anhydrous 0.6 g KH2PO4 monobasic;C: 250 mL RO H2O 4.68 g CaCl2 dihydrate;D: 250 mL RO H2O 6.15 g MgSO4·7H2O;E: 250 mL RO H2O 8.75 g NaHCO3. System water:purified water with sea salt and NaHCO3，conductivity 450 500 μs/cm，pH 7.0±0.2.	strain:AB\|tissue:kidney\|age:7 dpf /	GSM6532688	GSM6532688: 7d chd8 / zebrafish rep2; Danio rerio; RNA Seq	GSM6532688 r1	GSM6532688	1	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_chd8_2.fq.gz	fastq	5791321500.0	19304405.0	GSM6532688 r1	0:150 1:150	A:1504780584;C:1391586880;G:1405013206;T:1489820370;N:120460	150	150	1504780584	1391586880	1405013206	1489820370	120460	SRX17382861	SRS14941973			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95947	0.95202	0.07494	0.07307	0.71074	0.71163	0.45745	0.44001	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-08-31	Larval	Larval	Kidney	Renal System
69456	69456	SRR21377197	SRX17382860	SRS14941972	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.			7d chd8 / zebrafish rep1	GSM6532687	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf /	7d chd8 / zebrafish rep1	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	40 chd8 / zebrafish embryos at 5 dpf were collected and anesthetized in 0.4% 4g/L tricane. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h. The intestines were removed and collected by tweezers under the microscope and the isolated tissue was then transfered into Trizol. About 70 chd8 / zebrafish embryos at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane. Then the media were replaced with RNAlater RNA Solution and samples were storaged at 4℃ for more than 24h. Their kidneys were removed by tweezers under the microscope. Then the tissues were immersed in Trizol and the RNA of them were extracted as previously described for intestine tissues.	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with fish feeding circulation system water and allowed to mate for no more than 1 hour. Fertilized eggs were transfered into petri dishes less than 100 embryos per dish with embryo media. Then all of the embryos are incubated at 28.5℃ until the 5 dpf or 7 dpf. Embryo media:1L ddH2O with 10 ml stock solution A 1 mL stock solution B 10 mL stock solution C 10 mL stock solution D and 10 mL stock solution E adjust pH to 7.2 with 1 M HCl.A: 250 mL RO H2O 20 g NaCl 1 g KCl;B: 100 mL RO H2O 0.358 g Na2HPO4 anhydrous 0.6 g KH2PO4 monobasic;C: 250 mL RO H2O 4.68 g CaCl2 dihydrate;D: 250 mL RO H2O 6.15 g MgSO4·7H2O;E: 250 mL RO H2O 8.75 g NaHCO3. System water:purified water with sea salt and NaHCO3，conductivity 450 500 μs/cm，pH 7.0±0.2.	strain:AB\|tissue:kidney\|age:7 dpf /	GSM6532687	GSM6532687: 7d chd8 / zebrafish rep1; Danio rerio; RNA Seq	GSM6532687 r1	GSM6532687	1	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_chd8_1.fq.gz	fastq	5644382100.0	18814607.0	GSM6532687 r1	0:150 1:150	A:1422529122;C:1396709260;G:1413922498;T:1411168964;N:52256	150	150	1422529122	1396709260	1413922498	1411168964	52256	SRX17382860	SRS14941972			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.97204	0.96429	0.07483	0.07187	0.72064	0.72275	0.51419	0.5078	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-08-31	Larval	Larval	Kidney	Renal System
69460	69460	SRR18710063	SRX14810879	SRS12567670	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.			7d GF zebrafish rep3	GSM6038014	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf free	7d GF zebrafish rep3	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf free	GSM6038014	GSM6038014: 7d GF zebrafish rep3; Danio rerio; RNA Seq	GSM6038014 r1	GSM6038014	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_GF_3.fq.gz	fastq	5277204300.0	17590681.0	GSM6038014 r1	0:150 1:150	A:1366859942;C:1272510413;G:1282815853;T:1354917079;N:101013	150	150	1366859942	1272510413	1282815853	1354917079	101013	SRX14810879	SRS12567670			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.97097	0.96817	0.06893	0.06764	0.71603	0.71514	0.46915	0.46548	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69461	69461	SRR18710064	SRX14810878	SRS12567669	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.			7d GF zebrafish rep2	GSM6038013	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf free	7d GF zebrafish rep2	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf free	GSM6038013	GSM6038013: 7d GF zebrafish rep2; Danio rerio; RNA Seq	GSM6038013 r1	GSM6038013	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_GF_2.fq.gz	fastq	5438226900.0	18127423.0	GSM6038013 r1	0:150 1:150	A:1415418105;C:1302388066;G:1315056110;T:1404800640;N:563979	150	150	1415418105	1302388066	1315056110	1404800640	563979	SRX14810878	SRS12567669			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95347	0.95229	0.07185	0.06896	0.70674	0.70784	0.45432	0.45007	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69462	69462	SRR18710065	SRX14810877	SRS12567668	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.			7d GF zebrafish rep1	GSM6038012	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf free	7d GF zebrafish rep1	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf free	GSM6038012	GSM6038012: 7d GF zebrafish rep1; Danio rerio; RNA Seq	GSM6038012 r1	GSM6038012	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366	loader:fastq load.py\|options: concatPairFiles	7d_GF_1.fq.gz	fastq	5155842300.0	17186141.0	GSM6038012 r1	0:150 1:150	A:1336194101;C:1239856396;G:1253784751;T:1325279831;N:727221	150	150	1336194101	1239856396	1253784751	1325279831	727221	SRX14810877	SRS12567668			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95926	0.95555	0.07118	0.06919	0.70001	0.70116	0.43654	0.43125	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69463	69463	SRR18710066	SRX14810876	SRS12567667	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.			7d CV zebrafish rep3	GSM6038011	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf type	7d CV zebrafish rep3	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf type	GSM6038011	GSM6038011: 7d CV zebrafish rep3; Danio rerio; RNA Seq	GSM6038011 r1	GSM6038011	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366	loader:fastq load.py\|options: concatPairFiles	7d_CV_3.fq.gz	fastq	5141724000.0	17139080.0	GSM6038011 r1	0:150 1:150	A:1326004313;C:1239710760;G:1254841650;T:1320440570;N:726707	150	150	1326004313	1239710760	1254841650	1320440570	726707	SRX14810876	SRS12567667			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95248	0.95498	0.06745	0.06581	0.70078	0.70214	0.46456	0.46536	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69464	69464	SRR18710067	SRX14810875	SRS12567666	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.			7d CV zebrafish rep2	GSM6038010	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf type	7d CV zebrafish rep2	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf type	GSM6038010	GSM6038010: 7d CV zebrafish rep2; Danio rerio; RNA Seq	GSM6038010 r1	GSM6038010	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_CV_2.fq.gz	fastq	5661243900.0	18870813.0	GSM6038010 r1	0:150 1:150	A:1461910631;C:1369500371;G:1376299382;T:1453491360;N:42156	150	150	1461910631	1369500371	1376299382	1453491360	42156	SRX14810875	SRS12567666			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.96148	0.95899	0.06956	0.06718	0.7165	0.71683	0.46433	0.44486	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69465	69465	SRR18710068	SRX14810874	SRS12567665	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.			7d CV zebrafish rep1	GSM6038009	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf type	7d CV zebrafish rep1	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf type	GSM6038009	GSM6038009: 7d CV zebrafish rep1; Danio rerio; RNA Seq	GSM6038009 r1	GSM6038009	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_CV_1.fq.gz	fastq	5645537400.0	18818458.0	GSM6038009 r1	0:150 1:150	A:1445455143;C:1370729088;G:1387744819;T:1440941365;N:666985	150	150	1445455143	1370729088	1387744819	1440941365	666985	SRX14810874	SRS12567665			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95837	0.95913	0.06057	0.05807	0.72267	0.7236	0.4382	0.44735	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
74455	74455	SRR23804140	SRX19635460	SRS17004492	SRP426651	PRJNA943248	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]	GSE227115	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected homogenized filtered and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836		kdrl:GFP+ adult kidney	GSM7091842	source name:kdrl:GFP transgenic zebrafish adult kidney wild type\|developmental stage:adult\|genotype:wild type\|tissue:kidney	kdrl:GFP+ adult kidney	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:GFP transgenic zebrafish adult kidney wild type	No treatments	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer. Adult kidneys were dissected then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	developmental stage:adult\|genotype:wild type\|tissue:kidney	GSM7091842	GSM7091842: kdrl:GFP+ adult kidney; Danio rerio; RNA Seq	GSM7091842 r1	GSM7091842	1	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426651		FLK-G_Single_Cell_ACTCTAGG.fastq.sorted.fastq.gz	fastq	10648313404.0	80407702.0	GSM7091842 r1	0:132.43	A:3393628100;C:2087372845;G:1953079760;T:3213786135;N:446564	132		3393628100	2087372845	1953079760	3213786135	446564	SRX19635460	SRS17004492			Oncology/Hematology, Boston Children's Hospital	1	0.60891		0.10525		0.81903		0.52577		150		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Adult	Adult	Kidney	Renal System
74456	74456	SRR23804141	SRX19635459	SRS17004491	SRP426651	PRJNA943248	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]	GSE227115	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected homogenized filtered and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836		kdrl:mCherry+ adult kidney rep2	GSM7091841	source name:kdrl:mCherry transgenic zebrafish adult kidney wild type\|developmental stage:adult\|genotype:wild type\|tissue:kidney	kdrl:mCherry+ adult kidney rep2	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:mCherry transgenic zebrafish adult kidney wild type	No treatments	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer. Adult kidneys were dissected then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	developmental stage:adult\|genotype:wild type\|tissue:kidney	GSM7091841	GSM7091841: kdrl:mCherry+ adult kidney rep2; Danio rerio; RNA Seq	GSM7091841 r1	GSM7091841	1	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426651		FLK-R_Single_Cell_CTAGTCGA.fastq.sorted.fastq.gz	fastq	13922952441.0	105098464.0	GSM7091841 r1	0:132.48	A:4341235438;C:2807868369;G:2579519980;T:4193742000;N:586654	132		4341235438	2807868369	2579519980	4193742000	586654	SRX19635459	SRS17004491			Oncology/Hematology, Boston Children's Hospital	1	0.64512		0.12315		0.81712		0.52922		100		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Adult	Adult	Kidney	Renal System
74457	74457	SRR23804142	SRX19635458	SRS17004490	SRP426651	PRJNA943248	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]	GSE227115	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected homogenized filtered and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836		kdrl:mCherry+ adult kidney rep1	GSM7091840	source name:kdrl:mCherry transgenic zebrafish adult kidney wild type\|developmental stage:adult\|genotype:wild type\|tissue:kidney	kdrl:mCherry+ adult kidney rep1	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:mCherry transgenic zebrafish adult kidney wild type	No treatments	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer. Adult kidneys were dissected then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	developmental stage:adult\|genotype:wild type\|tissue:kidney	GSM7091840	GSM7091840: kdrl:mCherry+ adult kidney rep1; Danio rerio; RNA Seq	GSM7091840 r1	GSM7091840	1	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426651		KLR_Single_Cell_ATTAGACG.fastq.sorted.fastq.gz	fastq	8774502682.0	64692571.0	GSM7091840 r1	0:135.63	A:2791773089;C:1725088037;G:1633088372;T:2624197073;N:356111	135		2791773089	1725088037	1633088372	2624197073	356111	SRX19635458	SRS17004490			Oncology/Hematology, Boston Children's Hospital	1	0.66981		0.10372		0.81357		0.5394		38		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Adult	Adult	Kidney	Renal System
76969	76969	SRR25411155	SRX21146780	SRS18409873	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep2	GSM7659931	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep2	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659931	GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq	GSM7659931 r1	GSM7659931	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep2_CCGTCC_L001_R1_001.fastq.gz	fastq	204000000.0	4000000.0	GSM7659931 r1	0:51	A:53477924;C:49271060;G:48329809;T:52644666;N:276541	51		53477924	49271060	48329809	52644666	276541	SRX21146780	SRS18409873	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90949		0.04979		0.78616		0.46807		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76970	76970	SRR25411156	SRX21146780	SRS18409873	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep2	GSM7659931	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep2	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659931	GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq	GSM7659931 r1	GSM7659931	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep2_CCGTCC_L001_R1_002.fastq.gz	fastq	204000000.0	4000000.0	GSM7659931 r2	0:51	A:53509907;C:49243113;G:48349675;T:52646358;N:250947	51		53509907	49243113	48349675	52646358	250947	SRX21146780	SRS18409873	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90721		0.04855		0.78614		0.49297		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76971	76971	SRR25411157	SRX21146780	SRS18409873	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep2	GSM7659931	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep2	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659931	GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq	GSM7659931 r1	GSM7659931	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep2_CCGTCC_L001_R1_003.fastq.gz	fastq	184894839.0	3625389.0	GSM7659931 r3	0:51	A:48502504;C:44662414;G:43793127;T:47769015;N:167779	51		48502504	44662414	43793127	47769015	167779	SRX21146780	SRS18409873	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90939		0.04945		0.78413		0.50176		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76972	76972	SRR25411158	SRX21146780	SRS18409873	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep2	GSM7659931	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep2	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659931	GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq	GSM7659931 r1	GSM7659931	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep2_CCGTCC_L002_R1_001.fastq.gz	fastq	204000000.0	4000000.0	GSM7659931 r4	0:51	A:53524100;C:49307589;G:48369558;T:52683611;N:115142	51		53524100	49307589	48369558	52683611	115142	SRX21146780	SRS18409873	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90886		0.04911		0.78563		0.50213		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76973	76973	SRR25411159	SRX21146780	SRS18409873	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep2	GSM7659931	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep2	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659931	GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq	GSM7659931 r1	GSM7659931	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep2_CCGTCC_L002_R1_002.fastq.gz	fastq	204000000.0	4000000.0	GSM7659931 r5	0:51	A:53508602;C:49259259;G:48320396;T:52659338;N:252405	51		53508602	49259259	48320396	52659338	252405	SRX21146780	SRS18409873	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90952		0.04948		0.78476		0.50006		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76974	76974	SRR25411160	SRX21146780	SRS18409873	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep2	GSM7659931	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep2	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659931	GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq	GSM7659931 r1	GSM7659931	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep2_CCGTCC_L002_R1_003.fastq.gz	fastq	193938618.0	3802718.0	GSM7659931 r6	0:51	A:50925302;C:46847931;G:45921088;T:50125614;N:118683	51		50925302	46847931	45921088	50125614	118683	SRX21146780	SRS18409873	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90989		0.04933		0.78612		0.49518		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76975	76975	SRR25411161	SRX21146779	SRS18409872	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 mut rep1	GSM7659928	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 mut rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant	GSM7659928	GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq	GSM7659928 r1	GSM7659928	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_mut_rep1_AGTCAA_L001_R1_001.fastq.gz	fastq	204000000.0	4000000.0	GSM7659928 r1	0:51	A:55015856;C:47764328;G:46586189;T:54347107;N:286520	51		55015856	47764328	46586189	54347107	286520	SRX21146779	SRS18409872	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.94153		0.06397		0.7679		0.51518		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76976	76976	SRR25411162	SRX21146779	SRS18409872	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 mut rep1	GSM7659928	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 mut rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant	GSM7659928	GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq	GSM7659928 r1	GSM7659928	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_mut_rep1_AGTCAA_L001_R1_002.fastq.gz	fastq	204000000.0	4000000.0	GSM7659928 r2	0:51	A:55049694;C:47738867;G:46600712;T:54359486;N:251241	51		55049694	47738867	46600712	54359486	251241	SRX21146779	SRS18409872	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.93994		0.06362		0.76771		0.51436		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76977	76977	SRR25411163	SRX21146779	SRS18409872	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 mut rep1	GSM7659928	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 mut rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant	GSM7659928	GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq	GSM7659928 r1	GSM7659928	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_mut_rep1_AGTCAA_L001_R1_003.fastq.gz	fastq	184542582.0	3618482.0	GSM7659928 r3	0:51	A:49810884;C:43215836;G:42140250;T:49210846;N:164766	51		49810884	43215836	42140250	49210846	164766	SRX21146779	SRS18409872	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.94126		0.06349		0.76609		0.50688		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76978	76978	SRR25411164	SRX21146779	SRS18409872	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 mut rep1	GSM7659928	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 mut rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant	GSM7659928	GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq	GSM7659928 r1	GSM7659928	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_mut_rep1_AGTCAA_L002_R1_001.fastq.gz	fastq	204000000.0	4000000.0	GSM7659928 r4	0:51	A:55088455;C:47783649;G:46637795;T:54374341;N:115760	51		55088455	47783649	46637795	54374341	115760	SRX21146779	SRS18409872	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.94226		0.06408		0.76727		0.48927		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76979	76979	SRR25411165	SRX21146779	SRS18409872	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 mut rep1	GSM7659928	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 mut rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant	GSM7659928	GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq	GSM7659928 r1	GSM7659928	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_mut_rep1_AGTCAA_L002_R1_002.fastq.gz	fastq	204000000.0	4000000.0	GSM7659928 r5	0:51	A:55050408;C:47744731;G:46583753;T:54358628;N:262480	51		55050408	47744731	46583753	54358628	262480	SRX21146779	SRS18409872	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.94149		0.06416		0.7671		0.50616		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76980	76980	SRR25411166	SRX21146779	SRS18409872	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 mut rep1	GSM7659928	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 mut rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:TET2 mutant	GSM7659928	GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq	GSM7659928 r1	GSM7659928	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_mut_rep1_AGTCAA_L002_R1_003.fastq.gz	fastq	192468441.0	3773891.0	GSM7659928 r6	0:51	A:51989979;C:45058442;G:43960412;T:51339541;N:120067	51		51989979	45058442	43960412	51339541	120067	SRX21146779	SRS18409872	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.94177		0.06438		0.76751		0.50837		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76981	76981	SRR25411167	SRX21146778	SRS18409871	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep1	GSM7659930	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659930	GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq	GSM7659930 r1	GSM7659930	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep1_TGACCA_L001_R1_001.fastq.gz	fastq	204000000.0	4000000.0	GSM7659930 r1	0:51	A:54329942;C:48443007;G:47297646;T:53631114;N:298291	51		54329942	48443007	47297646	53631114	298291	SRX21146778	SRS18409871	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90366		0.06258		0.76958		0.48257		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76982	76982	SRR25411168	SRX21146778	SRS18409871	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep1	GSM7659930	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659930	GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq	GSM7659930 r1	GSM7659930	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep1_TGACCA_L001_R1_002.fastq.gz	fastq	204000000.0	4000000.0	GSM7659930 r2	0:51	A:54383177;C:48419596;G:47328645;T:53626949;N:241633	51		54383177	48419596	47328645	53626949	241633	SRX21146778	SRS18409871	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90117		0.06248		0.77064		0.51114		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76983	76983	SRR25411169	SRX21146778	SRS18409871	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep1	GSM7659930	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659930	GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq	GSM7659930 r1	GSM7659930	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep1_TGACCA_L001_R1_003.fastq.gz	fastq	204000000.0	4000000.0	GSM7659930 r3	0:51	A:54382835;C:48432142;G:47310240;T:53688971;N:185812	51		54382835	48432142	47310240	53688971	185812	SRX21146778	SRS18409871	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90404		0.06341		0.76962		0.48176		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76984	76984	SRR25411170	SRX21146778	SRS18409871	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep1	GSM7659930	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659930	GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq	GSM7659930 r1	GSM7659930	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep1_TGACCA_L001_R1_004.fastq.gz	fastq	22952397.0	450047.0	GSM7659930 r4	0:51	A:6123383;C:5438458;G:5312317;T:6056716;N:21523	51		6123383	5438458	5312317	6056716	21523	SRX21146778	SRS18409871	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90219		0.06393		0.77068		0.50827		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76985	76985	SRR25411171	SRX21146778	SRS18409871	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep1	GSM7659930	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659930	GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq	GSM7659930 r1	GSM7659930	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep1_TGACCA_L002_R1_001.fastq.gz	fastq	204000000.0	4000000.0	GSM7659930 r5	0:51	A:54377430;C:48474926;G:47349887;T:53685203;N:112554	51		54377430	48474926	47349887	53685203	112554	SRX21146778	SRS18409871	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90473		0.06338		0.77023		0.50688		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76986	76986	SRR25411172	SRX21146778	SRS18409871	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep1	GSM7659930	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659930	GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq	GSM7659930 r1	GSM7659930	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep1_TGACCA_L002_R1_002.fastq.gz	fastq	204000000.0	4000000.0	GSM7659930 r6	0:51	A:54337748;C:48437652;G:47307297;T:53646000;N:271303	51		54337748	48437652	47307297	53646000	271303	SRX21146778	SRS18409871	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.9051		0.06323		0.76966		0.50455		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76987	76987	SRR25411173	SRX21146778	SRS18409871	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep1	GSM7659930	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659930	GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq	GSM7659930 r1	GSM7659930	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep1_TGACCA_L002_R1_003.fastq.gz	fastq	204000000.0	4000000.0	GSM7659930 r7	0:51	A:54394822;C:48436830;G:47326355;T:53713847;N:128146	51		54394822	48436830	47326355	53713847	128146	SRX21146778	SRS18409871	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90342		0.06243		0.76917		0.51036		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	Renal System
76988	76988	SRR25411174	SRX21146778	SRS18409871	SRP451262	PRJNA998264	Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]	GSE238175	Transcriptome Analysis	Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effec…	parent bioproject:PRJNA998260	pubmed:37937078	RNAseq 4month tet2 wt rep1	GSM7659930	source name:Kidney\|tissue:Kidney\|cell type:marrow cells\|genotype:WT\|geo loc name:missing\|collection date:missing	RNAseq 4month tet2 wt rep1	Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene	Kidney		RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		tissue:Kidney\|cell type:marrow cells\|genotype:WT	GSM7659930	GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq	GSM7659930 r1	GSM7659930	1	RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP451262		RNAseq_4month_tet2_wt_rep1_TGACCA_L002_R1_004.fastq.gz	fastq	31292886.0	613586.0	GSM7659930 r8	0:51	A:8353864;C:7422258;G:7241468;T:8258321;N:16975	51		8353864	7422258	7241468	8258321	16975	SRX21146778	SRS18409871	SRA1679257	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia	1	0.90474		0.06355		0.77049		0.5033		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2023-07-25	Adult	Adult	Kidney	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");;