metadata: run_metadata: 12 rows where devstage_curation = "Adult" and experiment.library

12 rows where devstage_curation = "Adult" and experiment.library_selection = "Inverse rRNA"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
8108	8108	ERR2716246	ERX2730409	ERS2626924	ERP110098	PRJEB27957	Strand specific RNA sequencing of specific brain regions of the zebrafish	ena-STUDY-Biochemical Adaptation Laboratory-27-07-2018-11:07:45:884-1251	Other	Total RNA was isolated from three brain regions forebrain midbrain and hindbrain of wild type adult zebrafish Danio rerio. Strand specific RNA was sequenced post ribosomal depletion by Ribo Zero gold kit. Long non coding RNAs lncRNAs and mRNAs were detected and differential expression studied.	ENA FIRST PUBLIC:2018 09 26\|ENA LAST UPDATE:2018 07 27	Control forebrain RNA seq in zebrafish	Forebrain control	SAMEA4807015	Biochemical Adaptation Laboratory	ENA FIRST PUBLIC:2018 09 26T17:03:18Z\|ENA LAST UPDATE:2018 07 27T11:15:51Z\|External Id:SAMEA4807015\|INSDC center name:Biochemical Adaptation Laboratory\|INSDC first public:2018 09 26T17:03:18Z\|INSDC last update:2018 07 27T11:15:51Z\|INSDC status:public\|Submitter Id:Fbc2\|common name:zebrafish\|dev stage:adult\|sample name:Fbc2\|scientific name:Danio rerio\|tissue type:brain	Illumina NovaSeq 6000 paired end sequencing	ena EXPERIMENT Biochemical Adaptation Laboratory 27 07 2018 11:28:10:380 2	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP110098	Illumina NovaSeq 6000 paired end sequencing	ENA FIRST PUBLIC:2018 09 26\|ENA LAST UPDATE:2018 11 16	Fbc2_R1.fastq.gz Fbc2_R2.fastq.gz	fastq fastq	3163293134.0	15659867.0	ena RUN Biochemical Adaptation Laboratory 27 07 2018 11:28:10:380 2	0:101 1:101	A:902663616;C:674083265;G:685089226;T:901443399;N:13628	101	101	902663616	674083265	685089226	901443399	13628	ERX2730409	ERS2626924	ERA1552935	Biochemical Adaptation Laboratory\|European Nucleotide Archive	Biochemical Adaptation Laboratory	2	0.83256	0.83349	0.43782	0.43591	0.71514	0.71644	0.49741	0.48294	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	India	2018-07-27	Adult	Adult	Brain	Nervous System
8109	8109	ERR2716245	ERX2730408	ERS2626923	ERP110098	PRJEB27957	Strand specific RNA sequencing of specific brain regions of the zebrafish	ena-STUDY-Biochemical Adaptation Laboratory-27-07-2018-11:07:45:884-1251	Other	Total RNA was isolated from three brain regions forebrain midbrain and hindbrain of wild type adult zebrafish Danio rerio. Strand specific RNA was sequenced post ribosomal depletion by Ribo Zero gold kit. Long non coding RNAs lncRNAs and mRNAs were detected and differential expression studied.	ENA FIRST PUBLIC:2018 09 26\|ENA LAST UPDATE:2018 07 27	Control forebrain RNA seq in zebrafish	Forebrain control	SAMEA4807014	Biochemical Adaptation Laboratory	ENA FIRST PUBLIC:2018 09 26T17:03:18Z\|ENA LAST UPDATE:2018 07 27T11:15:46Z\|External Id:SAMEA4807014\|INSDC center name:Biochemical Adaptation Laboratory\|INSDC first public:2018 09 26T17:03:18Z\|INSDC last update:2018 07 27T11:15:46Z\|INSDC status:public\|Submitter Id:Fbc1\|common name:zebrafish\|dev stage:adult\|sample name:Fbc1\|scientific name:Danio rerio\|tissue type:brain	Illumina NovaSeq 6000 paired end sequencing	ena EXPERIMENT Biochemical Adaptation Laboratory 27 07 2018 11:28:10:379 1	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP110098	Illumina NovaSeq 6000 paired end sequencing	ENA FIRST PUBLIC:2018 09 26\|ENA LAST UPDATE:2018 11 16	Fbc1_R1.fastq.gz Fbc1_R2.fastq.gz	fastq fastq	3304372156.0	16358278.0	ena RUN Biochemical Adaptation Laboratory 27 07 2018 11:28:10:379 1	0:101 1:101	A:950810615;C:696498715;G:708600684;T:948447898;N:14244	101	101	950810615	696498715	708600684	948447898	14244	ERX2730408	ERS2626923	ERA1552935	Biochemical Adaptation Laboratory\|European Nucleotide Archive	Biochemical Adaptation Laboratory	2	0.46343	0.46503	0.21205	0.21055	0.7792	0.77674	0.4708	0.47581	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	India	2018-07-27	Adult	Adult	Brain	Nervous System
9812	9812	ERR3931362	ERX3938952	ERS4329529	ERP120057	PRJEB36819	Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	E-MTAB-8800	Transcriptome Analysis	Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.	ENA FIRST PUBLIC:2022 01 05\|ENA LAST UPDATE:2022 01 05	Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.	WKM 7 ED	SAMEA6565186	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA first public:2021 12 31\|ENA last update:2021 12 31\|External Id:SAMEA6565186\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2021 12 31T00:11:11Z\|INSDC last update:2021 12 31T00:11:11Z\|INSDC status:public\|Submitter Id:E MTAB 8800:WKM 7 ED\|broker name:ArrayExpress\|cell type:erythroid progenitor cell\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:Tg gata1:DsRed\|growth condition:Erythropoietin Dexamethas1\|individual:WKM7\|organism part:head kidney\|sample name:E MTAB 8800:WKM 7 ED	NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	E MTAB 8800:WKM 7 ED s	WKM 7 ED s	Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.	Experimental Factor: stimulus:n1	RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	SINGLE	ILLUMINA	NextSeq 500	ERP120057	NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	ENA FIRST PUBLIC:2022 01 05\|ENA LAST UPDATE:2022 01 05	10_WKM_7_ED.fastq.gz	fastq	3603783627.0	47724788.0	E MTAB 8800:WKM 7 ED	0:75.51 1:0	A:730277817;C:1059558661;G:1006087781;T:807771859;N:87509	75	0	730277817	1059558661	1006087781	807771859	87509	ERX3938952	ERS4329529	ERA2383450	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	1	0.96114		0.20335		0.83798		0.76524		76		B		usable mapping rate	illumina	nextseq	full_length	rrna_depletion	smarter	bulk	bulk	bulk	Czech Republic	2021-12-31	Adult	Adult	Multi-tissue	Multi-system
9813	9813	ERR3931361	ERX3938951	ERS4329528	ERP120057	PRJEB36819	Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	E-MTAB-8800	Transcriptome Analysis	Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.	ENA FIRST PUBLIC:2022 01 05\|ENA LAST UPDATE:2022 01 05	Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.	WKM 7 EaD	SAMEA6565185	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA first public:2021 12 31\|ENA last update:2021 12 31\|External Id:SAMEA6565185\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2021 12 31T00:11:11Z\|INSDC last update:2021 12 31T00:11:11Z\|INSDC status:public\|Submitter Id:E MTAB 8800:WKM 7 EaD\|broker name:ArrayExpress\|cell type:erythroid progenitor cell\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:Tg gata1:DsRed\|growth condition:Erythropoietin Dexamethas1\|individual:WKM7\|organism part:head kidney\|sample name:E MTAB 8800:WKM 7 EaD	NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	E MTAB 8800:WKM 7 EaD s	WKM 7 EaD s	Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.	Experimental Factor: stimulus:kit ligand	RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	SINGLE	ILLUMINA	NextSeq 500	ERP120057	NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	ENA FIRST PUBLIC:2022 01 05\|ENA LAST UPDATE:2022 01 05	11_WKM_7_EaD_1.fastq.gz	fastq	3127207407.0	41417754.0	E MTAB 8800:WKM 7 EaD	0:75.50 1:0	A:618290483;C:948661192;G:891134088;T:669046822;N:74822	75	0	618290483	948661192	891134088	669046822	74822	ERX3938951	ERS4329528	ERA2383450	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	1	0.96441		0.20171		0.85427		0.75425		76		B		usable mapping rate	illumina	nextseq	full_length	rrna_depletion	smarter	bulk	bulk	bulk	Czech Republic	2021-12-31	Adult	Adult	Multi-tissue	Multi-system
9814	9814	ERR3931360	ERX3938950	ERS4329527	ERP120057	PRJEB36819	Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	E-MTAB-8800	Transcriptome Analysis	Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.	ENA FIRST PUBLIC:2022 01 05\|ENA LAST UPDATE:2022 01 05	Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.	WKM 5 ED	SAMEA6565184	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA first public:2021 12 31\|ENA last update:2021 12 31\|External Id:SAMEA6565184\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2021 12 31T00:11:11Z\|INSDC last update:2021 12 31T00:11:11Z\|INSDC status:public\|Submitter Id:E MTAB 8800:WKM 5 ED\|broker name:ArrayExpress\|cell type:erythroid progenitor cell\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:Tg gata1:DsRed\|growth condition:Erythropoietin Dexamethas1\|individual:WKM5\|organism part:head kidney\|sample name:E MTAB 8800:WKM 5 ED	NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	E MTAB 8800:WKM 5 ED s	WKM 5 ED s	Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.	Experimental Factor: stimulus:n1	RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	SINGLE	ILLUMINA	NextSeq 500	ERP120057	NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	ENA FIRST PUBLIC:2022 01 05\|ENA LAST UPDATE:2022 01 05	8_WKM_5_ED.fastq.gz	fastq	3762435507.0	49825705.0	E MTAB 8800:WKM 5 ED	0:75.51 1:0	A:760573477;C:1107794761;G:1060998015;T:832975681;N:93573	75	0	760573477	1107794761	1060998015	832975681	93573	ERX3938950	ERS4329527	ERA2383450	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	1	0.96233		0.20628		0.84141		0.73601		75		B		usable mapping rate	illumina	nextseq	full_length	rrna_depletion	smarter	bulk	bulk	bulk	Czech Republic	2021-12-31	Adult	Adult	Multi-tissue	Multi-system
9815	9815	ERR3931359	ERX3938949	ERS4329526	ERP120057	PRJEB36819	Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	E-MTAB-8800	Transcriptome Analysis	Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.	ENA FIRST PUBLIC:2022 01 05\|ENA LAST UPDATE:2022 01 05	Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.	WKM 5 EaD	SAMEA6565183	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA first public:2021 12 31\|ENA last update:2021 12 31\|External Id:SAMEA6565183\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2021 12 31T00:11:11Z\|INSDC last update:2021 12 31T00:11:11Z\|INSDC status:public\|Submitter Id:E MTAB 8800:WKM 5 EaD\|broker name:ArrayExpress\|cell type:erythroid progenitor cell\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:Tg gata1:DsRed\|growth condition:Erythropoietin Dexamethas1\|individual:WKM5\|organism part:head kidney\|sample name:E MTAB 8800:WKM 5 EaD	NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	E MTAB 8800:WKM 5 EaD s	WKM 5 EaD s	Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.	Experimental Factor: stimulus:kit ligand	RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	SINGLE	ILLUMINA	NextSeq 500	ERP120057	NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga	ENA FIRST PUBLIC:2022 01 05\|ENA LAST UPDATE:2022 01 05	9_WKM_5_EaD.fastq.gz	fastq	3602342027.0	47707938.0	E MTAB 8800:WKM 5 EaD	0:75.51 1:0	A:717278291;C:1084375347;G:1027250408;T:773351695;N:86286	75	0	717278291	1084375347	1027250408	773351695	86286	ERX3938949	ERS4329526	ERA2383450	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	1	0.96461		0.20281		0.85303		0.74553		75		B		usable mapping rate	illumina	nextseq	full_length	rrna_depletion	smarter	bulk	bulk	bulk	Czech Republic	2021-12-31	Adult	Adult	Multi-tissue	Multi-system
11815	11815	ERR11799086	ERX11197445	ERS16222830	ERP149963	PRJEB64798	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E-MTAB-13228	Transcriptome Analysis	We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set	Sample 4	SAMEA114237385	Universite Libre de Bruxelles	ENA FIRST PUBLIC:2023 12 25T01:15:27Z\|ENA LAST UPDATE:2023 12 25T01:15:27Z\|External Id:SAMEA114237385\|INSDC center name:Universite Libre de Bruxelles\|INSDC first public:2023 12 25T01:15:27Z\|INSDC last update:2023 12 25T01:15:27Z\|INSDC status:public\|Submitter Id:E MTAB 13228:Sample 4\|age:6\|broker name:ArrayExpress\|cell type:microglial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:brain\|sample name:E MTAB 13228:Sample 4\|scientific name:Danio rerio\|sex:male and female\|strain:AB	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E MTAB 13228:Sample 4 p	Sample 4 p	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set		RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP149963	Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R1.fq.gz so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R2.fq.gz	fastq fastq	19305011730.0	95569365.0	E MTAB 13228:so zf94 VW4 MDMG7 CD45lo mhc2dab MGA S58 R	0:101 1:101	A:6768262250;C:3044091042;G:2847188942;T:6645295452;N:174044	101	101	6768262250	3044091042	2847188942	6645295452	174044	ERX11197445	ERS16222830	ERA26360556	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.57007	0.5231	0.45597	0.40582	0.91579	0.91674	0.58257	0.5625	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	unknown	bulk	bulk	bulk	United Kingdom	2023-12-25	Adult	Adult	Brain	Nervous System
11816	11816	ERR11799088	ERX11197447	ERS16222832	ERP149963	PRJEB64798	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E-MTAB-13228	Transcriptome Analysis	We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set	Sample 6	SAMEA114237387	Universite Libre de Bruxelles	ENA FIRST PUBLIC:2023 12 25T01:15:27Z\|ENA LAST UPDATE:2023 12 25T01:15:27Z\|External Id:SAMEA114237387\|INSDC center name:Universite Libre de Bruxelles\|INSDC first public:2023 12 25T01:15:27Z\|INSDC last update:2023 12 25T01:15:27Z\|INSDC status:public\|Submitter Id:E MTAB 13228:Sample 6\|age:6\|broker name:ArrayExpress\|cell type:myeloid leukocyte\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:brain\|sample name:E MTAB 13228:Sample 6\|scientific name:Danio rerio\|sex:male and female\|strain:AB	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E MTAB 13228:Sample 6 p	Sample 6 p	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set		RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP149963	Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R2.fq.gz so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R1.fq.gz	fastq fastq	21028230098.0	104100149.0	E MTAB 13228:so zf94 VW6 MDMF8 CD45hi mhc2dab MACA S60 R	0:101 1:101	A:6738894716;C:4007335499;G:3664578692;T:6617229148;N:192043	101	101	6738894716	4007335499	3664578692	6617229148	192043	ERX11197447	ERS16222832	ERA26360556	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.69217	0.69414	0.45934	0.4539	0.86423	0.86344	0.64485	0.62976	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	unknown	bulk	bulk	bulk	United Kingdom	2023-12-25	Adult	Adult	Brain	Nervous System
11817	11817	ERR11799085	ERX11197444	ERS16222829	ERP149963	PRJEB64798	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E-MTAB-13228	Transcriptome Analysis	We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set	Sample 3	SAMEA114237384	Universite Libre de Bruxelles	ENA FIRST PUBLIC:2023 12 25T01:15:27Z\|ENA LAST UPDATE:2023 12 25T01:15:27Z\|External Id:SAMEA114237384\|INSDC center name:Universite Libre de Bruxelles\|INSDC first public:2023 12 25T01:15:27Z\|INSDC last update:2023 12 25T01:15:27Z\|INSDC status:public\|Submitter Id:E MTAB 13228:Sample 3\|age:6\|broker name:ArrayExpress\|cell type:microglial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:brain\|sample name:E MTAB 13228:Sample 3\|scientific name:Danio rerio\|sex:male and female\|strain:AB	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E MTAB 13228:Sample 3 p	Sample 3 p	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set		RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP149963	Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R1.fq.gz so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R2.fq.gz	fastq fastq	20720724286.0	102577843.0	E MTAB 13228:so zf94 VW3 MDMG1 CD45lo mhc2dab MGA S57 R	0:101 1:101	A:7221245295;C:3305546836;G:3154595537;T:7039147315;N:189303	101	101	7221245295	3305546836	3154595537	7039147315	189303	ERX11197444	ERS16222829	ERA26360556	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.6027	0.56103	0.46397	0.41738	0.90536	0.90473	0.59858	0.59246	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	unknown	bulk	bulk	bulk	United Kingdom	2023-12-25	Adult	Adult	Brain	Nervous System
11818	11818	ERR11799087	ERX11197446	ERS16222831	ERP149963	PRJEB64798	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E-MTAB-13228	Transcriptome Analysis	We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set	Sample 5	SAMEA114237386	Universite Libre de Bruxelles	ENA FIRST PUBLIC:2023 12 25T01:15:27Z\|ENA LAST UPDATE:2023 12 25T01:15:27Z\|External Id:SAMEA114237386\|INSDC center name:Universite Libre de Bruxelles\|INSDC first public:2023 12 25T01:15:27Z\|INSDC last update:2023 12 25T01:15:27Z\|INSDC status:public\|Submitter Id:E MTAB 13228:Sample 5\|age:6\|broker name:ArrayExpress\|cell type:myeloid leukocyte\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:brain\|sample name:E MTAB 13228:Sample 5\|scientific name:Danio rerio\|sex:male and female\|strain:AB	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E MTAB 13228:Sample 5 p	Sample 5 p	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set		RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP149963	Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R2.fq.gz so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R1.fq.gz	fastq fastq	20557799368.0	101771284.0	E MTAB 13228:so zf94 VW5 MDMF2 CD45hi mhc2dab MACA S59 R	0:101 1:101	A:5872430236;C:4635392917;G:4244261404;T:5805533335;N:181476	101	101	5872430236	4635392917	4244261404	5805533335	181476	ERX11197446	ERS16222831	ERA26360556	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.48524	0.49426	0.30765	0.31318	0.87008	0.86918	0.60597	0.58678	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	unknown	bulk	bulk	bulk	United Kingdom	2023-12-25	Adult	Adult	Brain	Nervous System
11819	11819	ERR11799083	ERX11197442	ERS16222827	ERP149963	PRJEB64798	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E-MTAB-13228	Transcriptome Analysis	We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set	Sample 1	SAMEA114237382	Universite Libre de Bruxelles	ENA FIRST PUBLIC:2023 12 25T01:15:27Z\|ENA LAST UPDATE:2023 12 25T01:15:27Z\|External Id:SAMEA114237382\|INSDC center name:Universite Libre de Bruxelles\|INSDC first public:2023 12 25T01:15:27Z\|INSDC last update:2023 12 25T01:15:27Z\|INSDC status:public\|Submitter Id:E MTAB 13228:Sample 1\|age:6\|broker name:ArrayExpress\|cell type:microglial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:brain\|sample name:E MTAB 13228:Sample 1\|scientific name:Danio rerio\|sex:male and female\|strain:AB	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E MTAB 13228:Sample 1 p	Sample 1 p	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set		RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP149963	Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R2.fq.gz so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R1.fq.gz	fastq fastq	24592452226.0	121744813.0	E MTAB 13228:so zf94 VW1 P2Y12 CD45lo MGA S55 R	0:101 1:101	A:6964719283;C:5587681189;G:5075783189;T:6964040906;N:227659	101	101	6964719283	5587681189	5075783189	6964040906	227659	ERX11197442	ERS16222827	ERA26360556	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.82038	0.82668	0.39096	0.39605	0.82532	0.82446	0.63514	0.57014	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	unknown	bulk	bulk	bulk	United Kingdom	2023-12-25	Adult	Adult	Brain	Nervous System
11820	11820	ERR11799084	ERX11197443	ERS16222828	ERP149963	PRJEB64798	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E-MTAB-13228	Transcriptome Analysis	We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set	Sample 2	SAMEA114237383	Universite Libre de Bruxelles	ENA FIRST PUBLIC:2023 12 25T01:15:27Z\|ENA LAST UPDATE:2023 12 25T01:15:27Z\|External Id:SAMEA114237383\|INSDC center name:Universite Libre de Bruxelles\|INSDC first public:2023 12 25T01:15:27Z\|INSDC last update:2023 12 25T01:15:27Z\|INSDC status:public\|Submitter Id:E MTAB 13228:Sample 2\|age:6\|broker name:ArrayExpress\|cell type:microglial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:brain\|sample name:E MTAB 13228:Sample 2\|scientific name:Danio rerio\|sex:male and female\|strain:AB	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	E MTAB 13228:Sample 2 p	Sample 2 p	Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set		RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP149963	Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R2.fq.gz so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R1.fq.gz	fastq fastq	23692841994.0	117291297.0	E MTAB 13228:so zf94 VW2 P2Y12 CD45lo MGA S56 R	0:101 1:101	A:6997658831;C:5103576511;G:4615471075;T:6975924499;N:211078	101	101	6997658831	5103576511	4615471075	6975924499	211078	ERX11197443	ERS16222828	ERA26360556	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.78961	0.79279	0.39456	0.39476	0.8227	0.82309	0.62072	0.61776	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	unknown	bulk	bulk	bulk	United Kingdom	2023-12-25	Adult	Adult	Brain	Nervous System

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