metadata: run_metadata: 44 rows where devstage_curation = "Undetermined" and tissue

44 rows where devstage_curation = "Undetermined" and tissue_curation = "Blood"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	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.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
8092	8092	ERR2402432	ERX2443286	ERS2295360	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom MO rep3	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693977	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693977\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM12\|common name:zebrafish\|sample name:CM12\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 12	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM12.trimmed.read_1.fastq.gz CM12.trimmed.read_2.fastq.gz	fastq fastq	5384061477.0	38388598.0	ena RUN DPSQ 14 03 2018 19:09:09:420 12	0:70.70 1:69.55	A:1490429493;C:1197976503;G:1220014984;T:1475615043;N:25454	70	69	1490429493	1197976503	1220014984	1475615043	25454	ERX2443286	ERS2295360	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92285	0.9206	0.06862	0.0688	0.73983	0.74566	0.4752	0.49125	76	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8093	8093	ERR2402431	ERX2443285	ERS2295359	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom MO rep2	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693976	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693976\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM11\|common name:zebrafish\|sample name:CM11\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 11	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM11.trimmed.read_1.fastq.gz CM11.trimmed.read_2.fastq.gz	fastq fastq	5472085589.0	38860681.0	ena RUN DPSQ 14 03 2018 19:09:09:420 11	0:70.98 1:69.83	A:1514986213;C:1217661004;G:1240412104;T:1499000816;N:25452	70	69	1514986213	1217661004	1240412104	1499000816	25452	ERX2443285	ERS2295359	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91987	0.91874	0.0693	0.07042	0.74042	0.74629	0.48229	0.49144	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8094	8094	ERR2402430	ERX2443284	ERS2295358	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom MO rep1	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693975	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693975\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM10\|common name:zebrafish\|sample name:CM10\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 10	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM10.trimmed.read_1.fastq.gz CM10.trimmed.read_2.fastq.gz	fastq fastq	6091085806.0	43064771.0	ena RUN DPSQ 14 03 2018 19:09:09:420 10	0:71.33 1:70.11	A:1692450462;C:1348639943;G:1375433963;T:1674532019;N:29419	71	70	1692450462	1348639943	1375433963	1674532019	29419	ERX2443284	ERS2295358	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92184	0.92064	0.0699	0.0704	0.74286	0.74874	0.48978	0.48997	75	73	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8095	8095	ERR2402429	ERX2443283	ERS2295357	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom uninj rep3	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693974	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693974\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM9\|common name:zebrafish\|sample name:CM9\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 9	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM9.trimmed.read_1.fastq.gz CM9.trimmed.read_2.fastq.gz	fastq fastq	6329252570.0	45070159.0	ena RUN DPSQ 14 03 2018 19:09:09:420 9	0:70.79 1:69.64	A:1753489708;C:1407193617;G:1433449502;T:1735090181;N:29562	70	69	1753489708	1407193617	1433449502	1735090181	29562	ERX2443283	ERS2295357	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91683	0.91616	0.06775	0.06825	0.75158	0.75737	0.49386	0.49199	76	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8096	8096	ERR2402428	ERX2443282	ERS2295356	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom uninj rep2	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693973	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693973\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM8\|common name:zebrafish\|sample name:CM8\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 8	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM8.trimmed.read_1.fastq.gz CM8.trimmed.read_2.fastq.gz	fastq fastq	5405185494.0	38637007.0	ena RUN DPSQ 14 03 2018 19:09:09:420 8	0:70.45 1:69.44	A:1491577735;C:1206599147;G:1229354248;T:1477628006;N:26358	70	69	1491577735	1206599147	1229354248	1477628006	26358	ERX2443282	ERS2295356	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91776	0.91567	0.07134	0.07241	0.7517	0.75716	0.47952	0.48745	73	73	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8097	8097	ERR2402427	ERX2443281	ERS2295355	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom uninj rep1	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693972	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693972\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM7\|common name:zebrafish\|sample name:CM7\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 7	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM7.trimmed.read_1.fastq.gz CM7.trimmed.read_2.fastq.gz	fastq fastq	6262947202.0	44863127.0	ena RUN DPSQ 14 03 2018 19:09:09:420 7	0:70.28 1:69.32	A:1732018658;C:1394742098;G:1420957611;T:1715198292;N:30543	70	69	1732018658	1394742098	1420957611	1715198292	30543	ERX2443281	ERS2295355	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91622	0.9144	0.0754	0.07588	0.74886	0.75371	0.48672	0.48471	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8098	8098	ERR2402426	ERX2443280	ERS2295354	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het MO rep3	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693971	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693971\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM6\|common name:zebrafish\|sample name:CM6\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 6	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM6.trimmed.read_1.fastq.gz CM6.trimmed.read_2.fastq.gz	fastq fastq	5819615834.0	41591499.0	ena RUN DPSQ 14 03 2018 19:09:09:420 6	0:70.47 1:69.45	A:1594833553;C:1309877713;G:1335153588;T:1579722744;N:28236	70	69	1594833553	1309877713	1335153588	1579722744	28236	ERX2443280	ERS2295354	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92	0.9183	0.0573	0.05793	0.77362	0.778	0.47792	0.46987	76	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8099	8099	ERR2402425	ERX2443279	ERS2295353	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het MO rep2	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693970	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693970\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM5\|common name:zebrafish\|sample name:CM5\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 5	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM5.trimmed.read_1.fastq.gz CM5.trimmed.read_2.fastq.gz	fastq fastq	5573895202.0	39518227.0	ena RUN DPSQ 14 03 2018 19:09:09:420 5	0:71.02 1:70.03	A:1530297250;C:1251775796;G:1276506882;T:1515288256;N:27018	71	70	1530297250	1251775796	1276506882	1515288256	27018	ERX2443279	ERS2295353	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92217	0.92081	0.06807	0.06843	0.76926	0.77441	0.45543	0.48098	76	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8100	8100	ERR2402424	ERX2443278	ERS2295352	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het MO rep1	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693969	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693969\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM4\|common name:zebrafish\|sample name:CM4\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 4	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM4.trimmed.read_1.fastq.gz CM4.trimmed.read_2.fastq.gz	fastq fastq	5803404091.0	41335851.0	ena RUN DPSQ 14 03 2018 19:09:09:420 4	0:70.72 1:69.67	A:1590577583;C:1305683925;G:1331895549;T:1575219146;N:27888	70	69	1590577583	1305683925	1331895549	1575219146	27888	ERX2443278	ERS2295352	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.9216	0.91971	0.05719	0.05738	0.77333	0.77761	0.47789	0.47244	76	74	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8101	8101	ERR2402423	ERX2443277	ERS2295351	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het uninj rep3	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693968	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693968\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM3\|common name:zebrafish\|sample name:CM3\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 3	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM3.trimmed.read_1.fastq.gz CM3.trimmed.read_2.fastq.gz	fastq fastq	5992797058.0	42390223.0	ena RUN DPSQ 14 03 2018 19:09:09:420 3	0:71.26 1:70.11	A:1639390320;C:1352082344;G:1378624207;T:1622672043;N:28144	71	70	1639390320	1352082344	1378624207	1622672043	28144	ERX2443277	ERS2295351	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92104	0.92006	0.07044	0.07056	0.77506	0.78137	0.48154	0.46497	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8102	8102	ERR2402422	ERX2443276	ERS2295350	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het uninj rep2	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693967	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693967\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM2\|common name:zebrafish\|sample name:CM2\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 2	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM2.trimmed.read_2.fastq.gz CM2.trimmed.read_1.fastq.gz	fastq fastq	5611396868.0	39759688.0	ena RUN DPSQ 14 03 2018 19:09:09:420 2	0:71.11 1:70.02	A:1537234166;C:1262883447;G:1288444384;T:1522807333;N:27538	71	70	1537234166	1262883447	1288444384	1522807333	27538	ERX2443276	ERS2295350	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91881	0.91733	0.06861	0.06958	0.77238	0.77883	0.48415	0.47367	76	73	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8103	8103	ERR2402421	ERX2443275	ERS2295349	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het uninj rep1	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693966	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693966\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM1\|common name:zebrafish\|sample name:CM1\|scientific name:Danio rerio							NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 1	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM1.trimmed.read_1.fastq.gz CM1.trimmed.read_2.fastq.gz	fastq fastq	6229432533.0	44233290.0	ena RUN DPSQ 14 03 2018 19:09:09:420 1	0:70.98 1:69.85	A:1712806281;C:1395764700;G:1423415860;T:1697416127;N:29565	70	69	1712806281	1395764700	1423415860	1697416127	29565	ERX2443275	ERS2295349	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91818	0.9169	0.07104	0.07095	0.77585	0.78066	0.47896	0.46653	56	56	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
47869	47869	SRR6908743	SRX3856808	SRS3100400	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM9 eosinophils	GSM3070146		tissue:WKM9 eosinophils\|FISHid:WKM9\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM9 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM9 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM9\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070146	GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq	GSM3070146		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070146	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM9_eosinophils_L001_R1_001.fastq.gz WKM9_eosinophils_L001_R2_001.fastq.gz	fastq fastq	1378279915.0	9133302.0	GSM3070146 r1	0:75.43 1:75.48	A:398409215;C:214050926;G:243007260;T:522806293;N:6221	75	75	398409215	214050926	243007260	522806293	6221	SRX3856808	SRS3100400	SRA675960	GEO	Hubrecht Institute	2	0.32967	0.72245	0.27664	0.49284	0.96217	0.88688	0.44743	0.5676	76	73	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47870	47870	SRR6908744	SRX3856808	SRS3100400	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM9 eosinophils	GSM3070146		tissue:WKM9 eosinophils\|FISHid:WKM9\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM9 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM9 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM9\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070146	GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq	GSM3070146		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070146	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM9_eosinophils_L002_R1_001.fastq.gz WKM9_eosinophils_L002_R2_001.fastq.gz	fastq fastq	1347027331.0	8926023.0	GSM3070146 r2	0:75.43 1:75.48	A:386373331;C:208319487;G:242442973;T:509887930;N:3610	75	75	386373331	208319487	242442973	509887930	3610	SRX3856808	SRS3100400	SRA675960	GEO	Hubrecht Institute	2	0.32008	0.72405	0.26859	0.48848	0.96512	0.88791	0.46692	0.55937	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47871	47871	SRR6908745	SRX3856808	SRS3100400	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM9 eosinophils	GSM3070146		tissue:WKM9 eosinophils\|FISHid:WKM9\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM9 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM9 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM9\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070146	GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq	GSM3070146		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070146	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM9_eosinophils_L003_R1_001.fastq.gz WKM9_eosinophils_L003_R2_001.fastq.gz	fastq fastq	1241011911.0	8223327.0	GSM3070146 r3	0:75.44 1:75.48	A:356514159;C:192418351;G:221034567;T:471023588;N:21246	75	75	356514159	192418351	221034567	471023588	21246	SRX3856808	SRS3100400	SRA675960	GEO	Hubrecht Institute	2	0.31504	0.71934	0.26517	0.48722	0.96932	0.89499	0.47715	0.56814	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47872	47872	SRR6908746	SRX3856808	SRS3100400	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM9 eosinophils	GSM3070146		tissue:WKM9 eosinophils\|FISHid:WKM9\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM9 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM9 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM9\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070146	GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq	GSM3070146		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070146	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM9_eosinophils_L004_R1_001.fastq.gz WKM9_eosinophils_L004_R2_001.fastq.gz	fastq fastq	1199788386.0	7950347.0	GSM3070146 r4	0:75.44 1:75.47	A:343966384;C:184985849;G:216629920;T:454187010;N:19223	75	75	343966384	184985849	216629920	454187010	19223	SRX3856808	SRS3100400	SRA675960	GEO	Hubrecht Institute	2	0.32136	0.71802	0.27107	0.48741	0.97098	0.90057	0.4616	0.56009	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47917	47917	SRR6908693	SRX3856796	SRS3100388	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM4 eosinophils	GSM3070134		tissue:WKM4 eosinophils\|FISHid:WKM4\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM4 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM4 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM4\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070134	GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq	GSM3070134		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070134	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM4_eosinophils_L001_R1_001.fastq.gz WKM4_eosinophils_L001_R2_001.fastq.gz	fastq fastq	1044383799.0	6918578.0	GSM3070134 r1	0:75.49 1:75.46	A:293266328;C:159927306;G:179144897;T:412003143;N:42125	75	75	293266328	159927306	179144897	412003143	42125	SRX3856796	SRS3100388	SRA675960	GEO	Hubrecht Institute	2	0.38953	0.76677	0.33438	0.55076	0.94775	0.83664	0.47684	0.51667	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47918	47918	SRR6908694	SRX3856796	SRS3100388	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM4 eosinophils	GSM3070134		tissue:WKM4 eosinophils\|FISHid:WKM4\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM4 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM4 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM4\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070134	GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq	GSM3070134		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070134	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM4_eosinophils_L002_R1_001.fastq.gz WKM4_eosinophils_L002_R2_001.fastq.gz	fastq fastq	1065518294.0	7059081.0	GSM3070134 r2	0:75.49 1:75.45	A:299578147;C:162208243;G:185866185;T:417812882;N:52837	75	75	299578147	162208243	185866185	417812882	52837	SRX3856796	SRS3100388	SRA675960	GEO	Hubrecht Institute	2	0.36825	0.75817	0.3148	0.55624	0.95061	0.84794	0.47713	0.52081	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47919	47919	SRR6908695	SRX3856796	SRS3100388	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM4 eosinophils	GSM3070134		tissue:WKM4 eosinophils\|FISHid:WKM4\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM4 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM4 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM4\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070134	GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq	GSM3070134		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070134	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM4_eosinophils_L003_R1_001.fastq.gz WKM4_eosinophils_L003_R2_001.fastq.gz	fastq fastq	1020526841.0	6760661.0	GSM3070134 r3	0:75.50 1:75.45	A:287644655;C:155831653;G:174910820;T:402133481;N:6232	75	75	287644655	155831653	174910820	402133481	6232	SRX3856796	SRS3100388	SRA675960	GEO	Hubrecht Institute	2	0.38266	0.76495	0.32861	0.55487	0.94909	0.84502	0.47881	0.50844	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47920	47920	SRR6908696	SRX3856796	SRS3100388	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM4 eosinophils	GSM3070134		tissue:WKM4 eosinophils\|FISHid:WKM4\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM4 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM4 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM4\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070134	GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq	GSM3070134		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070134	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM4_eosinophils_L004_R2_001.fastq.gz WKM4_eosinophils_L004_R1_001.fastq.gz	fastq fastq	1036249497.0	6864317.0	GSM3070134 r4	0:75.50 1:75.46	A:290241796;C:157806083;G:180760457;T:407436042;N:5119	75	75	290241796	157806083	180760457	407436042	5119	SRX3856796	SRS3100388	SRA675960	GEO	Hubrecht Institute	2	0.38456	0.76284	0.32829	0.54843	0.9497	0.84668	0.48302	0.51789	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47925	47925	SRR6908685	SRX3856794	SRS3100386	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM3 eosinophils	GSM3070132		tissue:WKM3 eosinophils\|FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM3 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM3 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070132	GSM3070132: WKM3 eosinophils; Danio rerio; RNA Seq	GSM3070132		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070132	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM3_eosinophils_L001_R1_001.fastq.gz WKM3_eosinophils_L001_R2_001.fastq.gz	fastq fastq	1288630538.0	8538558.0	GSM3070132 r1	0:75.44 1:75.48	A:384649233;C:189860338;G:186795029;T:527108032;N:217906	75	75	384649233	189860338	186795029	527108032	217906	SRX3856794	SRS3100386	SRA675960	GEO	Hubrecht Institute	2	0.38213	0.80648	0.32	0.39443	0.96749	0.92997	0.49763	0.55351	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47926	47926	SRR6908686	SRX3856794	SRS3100386	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM3 eosinophils	GSM3070132		tissue:WKM3 eosinophils\|FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM3 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM3 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070132	GSM3070132: WKM3 eosinophils; Danio rerio; RNA Seq	GSM3070132		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070132	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM3_eosinophils_L002_R1_001.fastq.gz WKM3_eosinophils_L002_R2_001.fastq.gz	fastq fastq	1176806695.0	7797829.0	GSM3070132 r2	0:75.44 1:75.48	A:349406324;C:172751257;G:173925861;T:480558924;N:164329	75	75	349406324	172751257	173925861	480558924	164329	SRX3856794	SRS3100386	SRA675960	GEO	Hubrecht Institute	2	0.3792	0.81293	0.31911	0.39312	0.96834	0.93176	0.52878	0.54431	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47927	47927	SRR6908687	SRX3856794	SRS3100386	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM3 eosinophils	GSM3070132		tissue:WKM3 eosinophils\|FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM3 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM3 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070132	GSM3070132: WKM3 eosinophils; Danio rerio; RNA Seq	GSM3070132		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070132	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM3_eosinophils_L003_R1_001.fastq.gz WKM3_eosinophils_L003_R2_001.fastq.gz	fastq fastq	1341470236.0	8888024.0	GSM3070132 r3	0:75.45 1:75.48	A:395746232;C:196893713;G:196590339;T:552105050;N:134902	75	75	395746232	196893713	196590339	552105050	134902	SRX3856794	SRS3100386	SRA675960	GEO	Hubrecht Institute	2	0.38231	0.81774	0.3205	0.39891	0.97279	0.92817	0.47656	0.53862	75	74	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47928	47928	SRR6908688	SRX3856794	SRS3100386	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM3 eosinophils	GSM3070132		tissue:WKM3 eosinophils\|FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM3 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM3 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070132	GSM3070132: WKM3 eosinophils; Danio rerio; RNA Seq	GSM3070132		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070132	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM3_eosinophils_L004_R1_001.fastq.gz WKM3_eosinophils_L004_R2_001.fastq.gz	fastq fastq	1280409546.0	8484656.0	GSM3070132 r4	0:75.44 1:75.47	A:378449241;C:186686350;G:189951619;T:525218711;N:103625	75	75	378449241	186686350	189951619	525218711	103625	SRX3856794	SRS3100386	SRA675960	GEO	Hubrecht Institute	2	0.36531	0.80793	0.30661	0.38147	0.97492	0.94401	0.47223	0.55437	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47929	47929	SRR6908681	SRX3856793	SRS3100385	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM3 classicalgate eosinophils	GSM3070131		tissue:WKM3 classicalgate eosinophils\|FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	WKM3 classicalgate eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM3 classicalgate eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	GSM3070131	GSM3070131: WKM3 classicalgate eosinophils; Danio rerio; RNA Seq	GSM3070131		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070131	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM3_classicalgate-eosinophils_L001_R1_001.fastq.gz WKM3_classicalgate-eosinophils_L001_R2_001.fastq.gz	fastq fastq	1462702668.0	9694435.0	GSM3070131 r1	0:75.42 1:75.46	A:445709472;C:205316750;G:205641600;T:605784979;N:249867	75	75	445709472	205316750	205641600	605784979	249867	SRX3856793	SRS3100385	SRA675960	GEO	Hubrecht Institute	2	0.39724	0.82292	0.32577	0.36062	0.9713	0.9301	0.46129	0.54716	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47930	47930	SRR6908682	SRX3856793	SRS3100385	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM3 classicalgate eosinophils	GSM3070131		tissue:WKM3 classicalgate eosinophils\|FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	WKM3 classicalgate eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM3 classicalgate eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	GSM3070131	GSM3070131: WKM3 classicalgate eosinophils; Danio rerio; RNA Seq	GSM3070131		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070131	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM3_classicalgate-eosinophils_L002_R2_001.fastq.gz WKM3_classicalgate-eosinophils_L002_R1_001.fastq.gz	fastq fastq	1331127146.0	8822708.0	GSM3070131 r2	0:75.42 1:75.45	A:403738285;C:185977311;G:190160316;T:551055048;N:196186	75	75	403738285	185977311	190160316	551055048	196186	SRX3856793	SRS3100385	SRA675960	GEO	Hubrecht Institute	2	0.39004	0.81794	0.32291	0.35472	0.97228	0.93626	0.48683	0.54607	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47931	47931	SRR6908683	SRX3856793	SRS3100385	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM3 classicalgate eosinophils	GSM3070131		tissue:WKM3 classicalgate eosinophils\|FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	WKM3 classicalgate eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM3 classicalgate eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	GSM3070131	GSM3070131: WKM3 classicalgate eosinophils; Danio rerio; RNA Seq	GSM3070131		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070131	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM3_classicalgate-eosinophils_L003_R2_001.fastq.gz WKM3_classicalgate-eosinophils_L003_R1_001.fastq.gz	fastq fastq	1530092022.0	10140266.0	GSM3070131 r3	0:75.43 1:75.46	A:460384140;C:214158501;G:217473146;T:637914633;N:161602	75	75	460384140	214158501	217473146	637914633	161602	SRX3856793	SRS3100385	SRA675960	GEO	Hubrecht Institute	2	0.39487	0.82643	0.32278	0.35403	0.97555	0.92989	0.49836	0.55498	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47932	47932	SRR6908684	SRX3856793	SRS3100385	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM3 classicalgate eosinophils	GSM3070131		tissue:WKM3 classicalgate eosinophils\|FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	WKM3 classicalgate eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM3 classicalgate eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM3\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	GSM3070131	GSM3070131: WKM3 classicalgate eosinophils; Danio rerio; RNA Seq	GSM3070131		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070131	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM3_classicalgate-eosinophils_L004_R1_001.fastq.gz WKM3_classicalgate-eosinophils_L004_R2_001.fastq.gz	fastq fastq	1434145773.0	9505626.0	GSM3070131 r4	0:75.43 1:75.45	A:431807112;C:200115802;G:205473991;T:596630601;N:118267	75	75	431807112	200115802	205473991	596630601	118267	SRX3856793	SRS3100385	SRA675960	GEO	Hubrecht Institute	2	0.38268	0.82073	0.31346	0.34043	0.97678	0.94172	0.45791	0.5661	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47937	47937	SRR6908673	SRX3856790	SRS3100384	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM2 eosinophils	GSM3070129		tissue:WKM2 eosinophils\|FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM2 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM2 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070129	GSM3070129: WKM2 eosinophils; Danio rerio; RNA Seq	GSM3070129		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070129	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM2_eosinophils_L001_R1_001.fastq.gz WKM2_eosinophils_L001_R2_001.fastq.gz	fastq fastq	1444176720.0	9566997.0	GSM3070129 r1	0:75.46 1:75.50	A:432764637;C:224282941;G:222436448;T:564444426;N:248268	75	75	432764637	224282941	222436448	564444426	248268	SRX3856790	SRS3100384	SRA675960	GEO	Hubrecht Institute	2	0.37168	0.75194	0.32262	0.52753	0.95915	0.94073	0.51621	0.55453	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47938	47938	SRR6908674	SRX3856790	SRS3100384	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM2 eosinophils	GSM3070129		tissue:WKM2 eosinophils\|FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM2 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM2 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070129	GSM3070129: WKM2 eosinophils; Danio rerio; RNA Seq	GSM3070129		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070129	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM2_eosinophils_L002_R1_001.fastq.gz WKM2_eosinophils_L002_R2_001.fastq.gz	fastq fastq	1320784826.0	8749678.0	GSM3070129 r2	0:75.45 1:75.50	A:392835077;C:204358703;G:208201633;T:515202839;N:186574	75	75	392835077	204358703	208201633	515202839	186574	SRX3856790	SRS3100384	SRA675960	GEO	Hubrecht Institute	2	0.36921	0.73955	0.32271	0.52168	0.96047	0.94643	0.49733	0.53116	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47939	47939	SRR6908675	SRX3856790	SRS3100384	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM2 eosinophils	GSM3070129		tissue:WKM2 eosinophils\|FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM2 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM2 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070129	GSM3070129: WKM2 eosinophils; Danio rerio; RNA Seq	GSM3070129		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070129	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM2_eosinophils_L003_R2_001.fastq.gz WKM2_eosinophils_L003_R1_001.fastq.gz	fastq fastq	1500143635.0	9937133.0	GSM3070129 r3	0:75.46 1:75.50	A:445152171;C:231621688;G:233127317;T:590090278;N:152181	75	75	445152171	231621688	233127317	590090278	152181	SRX3856790	SRS3100384	SRA675960	GEO	Hubrecht Institute	2	0.36533	0.75138	0.31769	0.52682	0.96731	0.94209	0.50569	0.54346	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47940	47940	SRR6908676	SRX3856790	SRS3100384	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM2 eosinophils	GSM3070129		tissue:WKM2 eosinophils\|FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	WKM2 eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM2 eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:eosinophils	GSM3070129	GSM3070129: WKM2 eosinophils; Danio rerio; RNA Seq	GSM3070129		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070129	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM2_eosinophils_L004_R1_001.fastq.gz WKM2_eosinophils_L004_R2_001.fastq.gz	fastq fastq	1428668507.0	9464755.0	GSM3070129 r4	0:75.46 1:75.49	A:423108347;C:219338398;G:226517917;T:559587502;N:116343	75	75	423108347	219338398	226517917	559587502	116343	SRX3856790	SRS3100384	SRA675960	GEO	Hubrecht Institute	2	0.35962	0.7405	0.31464	0.51805	0.96962	0.95747	0.48862	0.53364	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47941	47941	SRR6908669	SRX3856789	SRS3100381	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM2 classicalgate eosinophils	GSM3070128		tissue:WKM2 classicalgate eosinophils\|FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	WKM2 classicalgate eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM2 classicalgate eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	GSM3070128	GSM3070128: WKM2 classicalgate eosinophils; Danio rerio; RNA Seq	GSM3070128		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070128	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM2_classicalgate-eosinophils_L001_R2_001.fastq.gz WKM2_classicalgate-eosinophils_L001_R1_001.fastq.gz	fastq fastq	880478792.0	5834816.0	GSM3070128 r1	0:75.43 1:75.47	A:267072322;C:127440559;G:126304290;T:359512123;N:149498	75	75	267072322	127440559	126304290	359512123	149498	SRX3856789	SRS3100381	SRA675960	GEO	Hubrecht Institute	2	0.3788	0.812	0.28918	0.38972	0.96595	0.92904	0.5376	0.55651	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47942	47942	SRR6908670	SRX3856789	SRS3100381	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM2 classicalgate eosinophils	GSM3070128		tissue:WKM2 classicalgate eosinophils\|FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	WKM2 classicalgate eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM2 classicalgate eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	GSM3070128	GSM3070128: WKM2 classicalgate eosinophils; Danio rerio; RNA Seq	GSM3070128		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070128	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM2_classicalgate-eosinophils_L002_R1_001.fastq.gz WKM2_classicalgate-eosinophils_L002_R2_001.fastq.gz	fastq fastq	806110283.0	5342262.0	GSM3070128 r2	0:75.42 1:75.47	A:243426891;C:116100169;G:117840212;T:328625621;N:117390	75	75	243426891	116100169	117840212	328625621	117390	SRX3856789	SRS3100381	SRA675960	GEO	Hubrecht Institute	2	0.38141	0.80952	0.29221	0.37995	0.96546	0.93381	0.54149	0.55378	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47943	47943	SRR6908671	SRX3856789	SRS3100381	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM2 classicalgate eosinophils	GSM3070128		tissue:WKM2 classicalgate eosinophils\|FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	WKM2 classicalgate eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM2 classicalgate eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	GSM3070128	GSM3070128: WKM2 classicalgate eosinophils; Danio rerio; RNA Seq	GSM3070128		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070128	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM2_classicalgate-eosinophils_L003_R1_001.fastq.gz WKM2_classicalgate-eosinophils_L003_R2_001.fastq.gz	fastq fastq	924045470.0	6123105.0	GSM3070128 r3	0:75.44 1:75.47	A:276824263;C:133108077;G:134012420;T:380008370;N:92340	75	75	276824263	133108077	134012420	380008370	92340	SRX3856789	SRS3100381	SRA675960	GEO	Hubrecht Institute	2	0.3819	0.81801	0.29161	0.38224	0.97124	0.92809	0.53982	0.54629	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
47944	47944	SRR6908672	SRX3856789	SRS3100381	SRP136633	PRJNA446034	Cell type purification by single cell transcriptome trained sorting	GSE112438	Other	Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.		pubmed:31585086		WKM2 classicalgate eosinophils	GSM3070128		tissue:WKM2 classicalgate eosinophils\|FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	WKM2 classicalgate eosinophils	In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode	WKM2 classicalgate eosinophils	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	FISHid:WKM2\|cell type:whole kidney marrow single cells\|cell subtype:classicalgate eosinophils	GSM3070128	GSM3070128: WKM2 classicalgate eosinophils; Danio rerio; RNA Seq	GSM3070128		1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters	GEO Accession:GSM3070128	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP136633			WKM2_classicalgate-eosinophils_L004_R1_001.fastq.gz WKM2_classicalgate-eosinophils_L004_R2_001.fastq.gz	fastq fastq	867397884.0	5748519.0	GSM3070128 r4	0:75.43 1:75.46	A:260294749;C:124376674;G:127341359;T:355314902;N:70200	75	75	260294749	124376674	127341359	355314902	70200	SRX3856789	SRS3100381	SRA675960	GEO	Hubrecht Institute	2	0.37148	0.80708	0.28632	0.3846	0.97299	0.94474	0.5375	0.54419	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Netherlands	2018-03-28	Undetermined	Undetermined	Blood	Hematopoietic System
52175	52175	SRR10902872	SRX7571042	SRS6006643	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.		pubmed:34660600		Blood 2	GSM4274618		source name:blood\|strain:Tubingen\|tissue:blood\|genotype:wild type	Blood 2	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	blood	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	strain:Tubingen\|tissue:blood\|genotype:wild type	GSM4274618	GSM4274618: Blood 2; Danio rerio; RNA Seq	GSM4274618		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM4274618	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254		assembly:GRCz10\|intentional duplicate	Blood2.bam	bam	31418773850.0	104035675.0	GSM4274618 r1	0:151 1:151	A:8027580943;C:5644210831;G:5587896051;T:12151089233;N:7996792	151	151	8027580943	5644210831	5587896051	12151089233	7996792	SRX7571042	SRS6006643	SRA880843	GEO	Zhejiang University	2	8e-05	0.56276	0.0	0.04786	0.99991	0.88363	0.75	0.53078	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2020-01-16	Undetermined	Multi-stage	Blood	Hematopoietic System
52176	52176	SRR10902871	SRX7571041	SRS6006642	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.		pubmed:34660600		Blood 1	GSM4274617		source name:blood\|strain:Tubingen\|tissue:blood\|genotype:wild type	Blood 1	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	blood	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	strain:Tubingen\|tissue:blood\|genotype:wild type	GSM4274617	GSM4274617: Blood 1; Danio rerio; RNA Seq	GSM4274617		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM4274617	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254		assembly:GRCz10\|intentional duplicate	Blood1.bam	bam	14970178354.0	49570127.0	GSM4274617 r1	0:151 1:151	A:3767585238;C:2725333545;G:2707312228;T:5766389198;N:3558145	151	151	3767585238	2725333545	2707312228	5766389198	3558145	SRX7571041	SRS6006642	SRA880843	GEO	Zhejiang University	2	0.0	0.58542	0.0	0.0298	1.0	0.89033		0.53826	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2020-01-16	Undetermined	Multi-stage	Blood	Hematopoietic System
67018	67018	SRR16973884	SRX13164748	SRS11095951	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.		pubmed:35502759		HSC mut rep3 RNA	GSM5694258		tissue:hematopoietic stem cells\|developmental stage:HSC\|genotype:dnmt1 mutant\|region:AGM	HSC mut rep3 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hematopoietic stem cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HSC\|genotype:dnmt1 mutant\|region:AGM	GSM5694258	GSM5694258: HSC mut rep3 RNA; Danio rerio; RNA Seq	GSM5694258		1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		loader:fastq load.py	HSC_sib_3_1_RNA.fq.gz HSC_sib_3_2_RNA.fq.gz	fastq fastq	8212205400.0	27374018.0	GSM5694258 r1	0:150 1:150	A:2309633599;C:1667340979;G:1773247570;T:2461956533;N:26719	150	150	2309633599	1667340979	1773247570	2461956533	26719	SRX13164748	SRS11095951	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.9402	0.93297	0.16899	0.16784	0.73089	0.73665	0.49638	0.49263	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Blood	Hematopoietic System
67019	67019	SRR16973883	SRX13164747	SRS11095950	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.		pubmed:35502759		HSC mut rep2 RNA	GSM5694257		tissue:hematopoietic stem cells\|developmental stage:HSC\|genotype:dnmt1 mutant\|region:AGM	HSC mut rep2 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hematopoietic stem cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HSC\|genotype:dnmt1 mutant\|region:AGM	GSM5694257	GSM5694257: HSC mut rep2 RNA; Danio rerio; RNA Seq	GSM5694257		1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694257	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708			HSC_sib_2_1_RNA.fq.gz HSC_sib_2_2_RNA.fq.gz	fastq fastq	3426398100.0	11421327.0	GSM5694257 r1	0:150 1:150	A:946653601;C:712946549;G:748099225;T:1018648813;N:49912	150	150	946653601	712946549	748099225	1018648813	49912	SRX13164747	SRS11095950	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.94198	0.95128	0.10797	0.10975	0.78366	0.78892	0.46218	0.45981	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Blood	Hematopoietic System
67020	67020	SRR16973881	SRX13164745	SRS11095948	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.		pubmed:35502759		HSC sib rep3 RNA	GSM5694255		tissue:hematopoietic stem cells\|developmental stage:HSC\|genotype:sibling\|region:AGM	HSC sib rep3 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hematopoietic stem cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HSC\|genotype:sibling\|region:AGM	GSM5694255	GSM5694255: HSC sib rep3 RNA; Danio rerio; RNA Seq	GSM5694255		1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		loader:fastq load.py	HSC_mut_3_1_RNA.fq.gz HSC_mut_3_2_RNA.fq.gz	fastq fastq	9049492800.0	30164976.0	GSM5694255 r1	0:150 1:150	A:2539831836;C:1839829118;G:1955216925;T:2714585195;N:29726	150	150	2539831836	1839829118	1955216925	2714585195	29726	SRX13164745	SRS11095948	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.94274	0.93556	0.16188	0.1602	0.73046	0.73308	0.49974	0.49435	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Blood	Hematopoietic System
67021	67021	SRR16973880	SRX13164744	SRS11095947	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.		pubmed:35502759		HSC sib rep2 RNA	GSM5694254		tissue:hematopoietic stem cells\|developmental stage:HSC\|genotype:sibling\|region:AGM	HSC sib rep2 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hematopoietic stem cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HSC\|genotype:sibling\|region:AGM	GSM5694254	GSM5694254: HSC sib rep2 RNA; Danio rerio; RNA Seq	GSM5694254		1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708			HSC_mut_2_1_RNA.fq.gz HSC_mut_2_2_RNA.fq.gz	fastq fastq	3488203500.0	11627345.0	GSM5694254 r1	0:150 1:150	A:993927631;C:700449875;G:737230481;T:1056544435;N:51078	150	150	993927631	700449875	737230481	1056544435	51078	SRX13164744	SRS11095947	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.93176	0.93765	0.14294	0.14478	0.75302	0.7582	0.49038	0.48496	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Blood	Hematopoietic System
76585	76585	SRR25181149	SRX20928872	SRS18204809	SRP447851	PRJNA991987	RNA seq for gata1+ cells in add1 mutant zebrafish embryos and siblings at 22 hpf	GSE236659	Transcriptome Analysis	Adducin 1 Add1 functions primarily as a membrane cytoskeletal protein whereas Add1 contains a bipartite nuclear localization signal implying its special nuclear function. However the nuclear functional roles of Add1 apart from maintaining cytoskeletal stability remain unknown. Here we created add1 deficient zebrafish using Tol2 transposon mediated gene trapping and evaluated how add1 deficiency affected early hematopoiesis development. When add1 is lacking in zebrafish both the primitive erythropoiesis and definitive hematopoiesis are compromised and the primitive erythroblast cells are unable to develop into healthy erythrocytes. More significantly the RNA sequencing results demonstrated that the p53 pathway is activated in the add1 depletion erythroblast cells causing the erythroblasts to undergo apoptosis at the 14 somites stage and 24 hpf. Additionally the anemic phenotype and apoptosis in add1 deficient embryos can be partially rescued by p53 insufficiency. Taken together our findings show that add1 is critical for zebrafish erythropoiesis partially through the p53 mediated apoptotic pathway which expands the regulatory role of Add1 for nuclear function. Overall design: To better understand the nuclear specific function of add1 we used RNA seq to analyze transcriptome changes in gata1 EGFP positive cells sorted from add1 deficient embryos and siblings at 22 hpf when the differences in the number of erythrocytes were not yet evident in add1 mutant embryos. Comparative gene expression profiling analysis of RNA seq data for erythroblast of add1 mutant and siblings.		pubmed:37636049		WT	GSM7567236		tissue:erythroblast\|cell type:erythroblast\|genotype:wildtype\|geo loc name:missing\|collection date:missing	WT	For gene expression analysis the matched reads were calculated and then normalized to RPKM using RESM software The significance of the differential expression of genes was defined by the bioinformatics service of BGI according to the combination of the absolute value of log2 Ratio ≥1 and FDR ≤ 0.001. Library construction and sequencing were performed on a BGISEQ 500. Assembly: GRCz10.81 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file include RPKM values for each Sample	erythroblast	Total RNA was isolated using SMART Seq® HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.	cell type:erythroblast\|genotype:wildtype	GSM7567236	GSM7567236: WT; Danio rerio; RNA Seq	GSM7567236 r1	GSM7567236	1	Total RNA was isolated using SMART Seq® HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP447851			WT_1.fq.gz WT_2.fq.gz	fastq fastq	6503251500.0	21677505.0	GSM7567236 r1	0:150 1:150	A:1785076844;C:1448752781;G:1570097457;T:1699269694;N:54724	150	150	1785076844	1448752781	1570097457	1699269694	54724	SRX20928872	SRS18204809			Children's Hospital of Capital Institute of Pediatrics	2	0.94793	0.94488	0.07407	0.07319	0.75493	0.75578	0.45437	0.45369	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-07-06	Undetermined	Embryo	Blood	Hematopoietic System
76586	76586	SRR25181150	SRX20928871	SRS18204814	SRP447851	PRJNA991987	RNA seq for gata1+ cells in add1 mutant zebrafish embryos and siblings at 22 hpf	GSE236659	Transcriptome Analysis	Adducin 1 Add1 functions primarily as a membrane cytoskeletal protein whereas Add1 contains a bipartite nuclear localization signal implying its special nuclear function. However the nuclear functional roles of Add1 apart from maintaining cytoskeletal stability remain unknown. Here we created add1 deficient zebrafish using Tol2 transposon mediated gene trapping and evaluated how add1 deficiency affected early hematopoiesis development. When add1 is lacking in zebrafish both the primitive erythropoiesis and definitive hematopoiesis are compromised and the primitive erythroblast cells are unable to develop into healthy erythrocytes. More significantly the RNA sequencing results demonstrated that the p53 pathway is activated in the add1 depletion erythroblast cells causing the erythroblasts to undergo apoptosis at the 14 somites stage and 24 hpf. Additionally the anemic phenotype and apoptosis in add1 deficient embryos can be partially rescued by p53 insufficiency. Taken together our findings show that add1 is critical for zebrafish erythropoiesis partially through the p53 mediated apoptotic pathway which expands the regulatory role of Add1 for nuclear function. Overall design: To better understand the nuclear specific function of add1 we used RNA seq to analyze transcriptome changes in gata1 EGFP positive cells sorted from add1 deficient embryos and siblings at 22 hpf when the differences in the number of erythrocytes were not yet evident in add1 mutant embryos. Comparative gene expression profiling analysis of RNA seq data for erythroblast of add1 mutant and siblings.		pubmed:37636049		MT	GSM7567235		tissue:erythroblast\|cell type:erythroblast\|genotype:add1 knockout\|geo loc name:missing\|collection date:missing	MT	For gene expression analysis the matched reads were calculated and then normalized to RPKM using RESM software The significance of the differential expression of genes was defined by the bioinformatics service of BGI according to the combination of the absolute value of log2 Ratio ≥1 and FDR ≤ 0.001. Library construction and sequencing were performed on a BGISEQ 500. Assembly: GRCz10.81 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file include RPKM values for each Sample	erythroblast	Total RNA was isolated using SMART Seq® HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.	cell type:erythroblast\|genotype:add1 knockout	GSM7567235	GSM7567235: MT; Danio rerio; RNA Seq	GSM7567235 r1	GSM7567235	1	Total RNA was isolated using SMART Seq® HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP447851			MT_1.fq.gz MT_2.fq.gz	fastq fastq	5929551300.0	19765171.0	GSM7567235 r1	0:150 1:150	A:1637382549;C:1315432930;G:1401397872;T:1575277995;N:59954	150	150	1637382549	1315432930	1401397872	1575277995	59954	SRX20928871	SRS18204814			Children's Hospital of Capital Institute of Pediatrics	2	0.94579	0.94497	0.08957	0.08915	0.7315	0.7329	0.44901	0.45809	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-07-06	Undetermined	Embryo	Blood	Hematopoietic 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");;