metadata: run_metadata: 6 rows where technology = "indrops" and tissue

6 rows where technology = "indrops" and tissue_curation = "Tail"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
32781	32781	SRR29411985	SRX24925451	SRS21630866	SRP513930	PRJNA1124008	Cell state transitions are decoupled from cell division during early embryo development [II]	GSE269848	Other	Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa…		pubmed:37546736	24 38 hpf and 48 hpf tails	GSM8328864	source name:embryo tail\|tissue:embryo tail\|geo loc name:missing\|collection date:missing	24 38 hpf and 48 hpf tails	Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f…	embryo tail		Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.		tissue:embryo tail	GSM8328864	GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER	GSM8328864 r1	GSM8328864	1	Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP513930	Undetermined_S0_L002_R1_001.fastq.gz Undetermined_S0_L002_R2_001.fastq.gz Undetermined_S0_L002_R3_001.fastq.gz Undetermined_S0_L002_R4_001.fastq.gz	fastq fastq fastq fastq	58603546956.0	505202991.0	GSM8328864 r1	0:86 1:8 2:8 3:14	A:13191204330;C:9162028793;G:9431065581;T:11662090182;N:1068340	86	8	8	14	13191204330	9162028793	9431065581	11662090182	1068340	SRX24925451	SRS21630866	SRA1899240	Harvard University	Harvard University							B	usable mapping rate	illumina	novaseq_era	unknown	other	trueseq	sc	single_cell_droplet	indrops	United States	2024-06-14	Multi-stage	Embryo	Tail	Multi-system
32782	32782	SRR29411986	SRX24925451	SRS21630866	SRP513930	PRJNA1124008	Cell state transitions are decoupled from cell division during early embryo development [II]	GSE269848	Other	Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa…		pubmed:37546736	24 38 hpf and 48 hpf tails	GSM8328864	source name:embryo tail\|tissue:embryo tail\|geo loc name:missing\|collection date:missing	24 38 hpf and 48 hpf tails	Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f…	embryo tail		Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.		tissue:embryo tail	GSM8328864	GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER	GSM8328864 r1	GSM8328864	1	Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP513930	Undetermined_S0_L001_R1_001.fastq.gz Undetermined_S0_L001_R2_001.fastq.gz Undetermined_S0_L001_R3_001.fastq.gz Undetermined_S0_L001_R4_001.fastq.gz	fastq fastq fastq fastq	44072422880.0	379934680.0	GSM8328864 r2	0:86 1:8 2:8 3:14	A:9919784228;C:6894965731;G:7094749745;T:8764100624;N:782152	86	8	8	14	9919784228	6894965731	7094749745	8764100624	782152	SRX24925451	SRS21630866	SRA1899240	Harvard University	Harvard University							B	usable mapping rate	illumina	novaseq_era	unknown	other	trueseq	sc	single_cell_droplet	indrops	United States	2024-06-14	Multi-stage	Embryo	Tail	Multi-system
74460	74460	SRR23802569	SRX19634451	SRS17003621	SRP426621	PRJNA943252	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]	GSE227118	Other	We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836		Whole tail 72 hpf	GSM7091920	source name:transgenic zebrafish embryos wild type\|tissue:Whole tail\|developmental stage:72 hpf	Whole tail 72 hpf	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	transgenic zebrafish embryos wild type	No treatments	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells.	tissue:Whole tail\|developmental stage:72 hpf	GSM7091920	GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq	GSM7091920 r1	GSM7091920	1	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426621	EH_Tails_Single_Cell_GAGACGGA_L001.fastq.sorted.fastq.gz	fastq	715456535.0	12017381.0	GSM7091920 r1	0:59.54	A:205982879;C:141307848;G:135221384;T:232940601;N:3823	59				205982879	141307848	135221384	232940601	3823	SRX19634451	SRS17003621			Oncology/Hematology, Boston Children's Hospital	1	0.88315	0.14516	0.78257	0.49661	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Tail	Multi-system
74461	74461	SRR23802570	SRX19634451	SRS17003621	SRP426621	PRJNA943252	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]	GSE227118	Other	We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836		Whole tail 72 hpf	GSM7091920	source name:transgenic zebrafish embryos wild type\|tissue:Whole tail\|developmental stage:72 hpf	Whole tail 72 hpf	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	transgenic zebrafish embryos wild type	No treatments	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells.	tissue:Whole tail\|developmental stage:72 hpf	GSM7091920	GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq	GSM7091920 r1	GSM7091920	1	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426621	EH_Tails_Single_Cell_GAGACGGA_L002.fastq.sorted.fastq.gz	fastq	589786185.0	9927008.0	GSM7091920 r2	0:59.41	A:170171480;C:115960508;G:111370241;T:192283114;N:842	59				170171480	115960508	111370241	192283114	842	SRX19634451	SRS17003621			Oncology/Hematology, Boston Children's Hospital	1	0.88418	0.1452	0.78173	0.48617	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Tail	Multi-system
74462	74462	SRR23802571	SRX19634451	SRS17003621	SRP426621	PRJNA943252	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]	GSE227118	Other	We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836		Whole tail 72 hpf	GSM7091920	source name:transgenic zebrafish embryos wild type\|tissue:Whole tail\|developmental stage:72 hpf	Whole tail 72 hpf	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	transgenic zebrafish embryos wild type	No treatments	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells.	tissue:Whole tail\|developmental stage:72 hpf	GSM7091920	GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq	GSM7091920 r1	GSM7091920	1	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426621	EH_Tails_Single_Cell_GAGACGGA_L003.fastq.sorted.fastq.gz	fastq	683131915.0	11477240.0	GSM7091920 r3	0:59.52	A:196805573;C:134822600;G:129142852;T:222358115;N:2775	59				196805573	134822600	129142852	222358115	2775	SRX19634451	SRS17003621			Oncology/Hematology, Boston Children's Hospital	1	0.88169	0.14457	0.78054	0.49459	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Tail	Multi-system
74463	74463	SRR23802572	SRX19634451	SRS17003621	SRP426621	PRJNA943252	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]	GSE227118	Other	We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836		Whole tail 72 hpf	GSM7091920	source name:transgenic zebrafish embryos wild type\|tissue:Whole tail\|developmental stage:72 hpf	Whole tail 72 hpf	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	transgenic zebrafish embryos wild type	No treatments	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells.	tissue:Whole tail\|developmental stage:72 hpf	GSM7091920	GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq	GSM7091920 r1	GSM7091920	1	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426621	EH_Tails_Single_Cell_GAGACGGA_L004.fastq.sorted.fastq.gz	fastq	584432554.0	9840065.0	GSM7091920 r4	0:59.39	A:168684456;C:114891950;G:110562368;T:190292465;N:1315	59				168684456	114891950	110562368	190292465	1315	SRX19634451	SRS17003621			Oncology/Hematology, Boston Children's Hospital	1	0.88266	0.14397	0.78001	0.49223	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Tail	Multi-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");;