metadata: run_metadata: 8 rows where experiment.library_selection = "Inverse rRNA", experiment.library_source = "TRANSCRIPTOMIC" and tissue

8 rows where experiment.library_selection = "Inverse rRNA", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Brain"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.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.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
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");;