metadata: run_metadata: 7 rows where devstage_curation_coarse = "Adult" and technology = "marsseq"

7 rows where devstage_curation_coarse = "Adult" and technology = "marsseq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	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
68656	68656	SRR18097957	SRX14248907	SRS12068875	SRP360907	PRJNA809307	Generation of specialized blood vessels via lymphatic transdifferentiation	GSE197161	Transcriptome Analysis	The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells	pubmed:35614218	Immature fin ECs plate3	GSM5910460	source name:fli1a:dsRed positive cells\|tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	Immature fin ECs plate3	GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names	fli1a:dsRed positive cells		80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014		tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	GSM5910460	GSM5910460: Immature fin ECs plate3; Danio rerio; RNA Seq	GSM5910460 r1	GSM5910460	1	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP360907		BC3_S0_R1_001.fastq.gz BC3_S0_R2_001.fastq.gz	fastq fastq	5000226570.0	55558073.0	GSM5910460 r1	0:75 1:15	A:1398279779;C:1105834990;G:1278168650;T:1217071842;N:871309	75	15	1398279779	1105834990	1278168650	1217071842	871309	SRX14248907	SRS12068875	SRA1376737	Weizmann Institute of Science	Department of Biological Regulation, Weizmann Institute of Science	2	0.75587	0.22384	0.87665	1.0	0.59533	75	15	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-02-22	Undetermined	Adult	Fin	Surface Structure
68657	68657	SRR18097958	SRX14248906	SRS12068874	SRP360907	PRJNA809307	Generation of specialized blood vessels via lymphatic transdifferentiation	GSE197161	Transcriptome Analysis	The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells	pubmed:35614218	Immature fin ECs plate2	GSM5910459	source name:fli1a:dsRed positive cells\|tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	Immature fin ECs plate2	GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names	fli1a:dsRed positive cells		80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014		tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	GSM5910459	GSM5910459: Immature fin ECs plate2; Danio rerio; RNA Seq	GSM5910459 r1	GSM5910459	1	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP360907		BC2_S0_R1_001.fastq.gz BC2_S0_R2_001.fastq.gz	fastq fastq	4158365400.0	46204060.0	GSM5910459 r1	0:75 1:15	A:1056133752;C:954371027;G:1117373354;T:1029764959;N:722308	75	15	1056133752	954371027	1117373354	1029764959	722308	SRX14248906	SRS12068874	SRA1376737	Weizmann Institute of Science	Department of Biological Regulation, Weizmann Institute of Science	2	0.76282	0.2382	0.87158	1.0	0.53888	75	15	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-02-22	Undetermined	Adult	Fin	Surface Structure
68658	68658	SRR18097959	SRX14248905	SRS12068873	SRP360907	PRJNA809307	Generation of specialized blood vessels via lymphatic transdifferentiation	GSE197161	Transcriptome Analysis	The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells	pubmed:35614218	Immature fin ECs plate1	GSM5910458	source name:fli1a:dsRed positive cells\|tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	Immature fin ECs plate1	GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names	fli1a:dsRed positive cells		80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014		tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	GSM5910458	GSM5910458: Immature fin ECs plate1; Danio rerio; RNA Seq	GSM5910458 r1	GSM5910458	1	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP360907		BC1_S0_R1_001.fastq.gz BC1_S0_R2_001.fastq.gz	fastq fastq	4284501750.0	47605575.0	GSM5910458 r1	0:75 1:15	A:1172578653;C:976724863;G:1071723716;T:1062724053;N:750465	75	15	1172578653	976724863	1071723716	1062724053	750465	SRX14248905	SRS12068873	SRA1376737	Weizmann Institute of Science	Department of Biological Regulation, Weizmann Institute of Science	2	0.73652	0.20176	0.86622	1.0	0.66697	75	15	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-02-22	Undetermined	Adult	Fin	Surface Structure
69988	69988	SRR19217299	SRX15281308	SRS13012753	SRP375342	PRJNA838481	Neural plate progenitors give rise to both anterior and posterior pituitary cells	GSE203075	Transcriptome Analysis	The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.	pubmed:37683631	AB9278	GSM6153483	source name:Neurohypophysis enriched cells\|strain:AB Tgpomca:EGFP\|tissue:Neurohypophysis\|age:7 month\|geo loc name:missing\|collection date:missing	AB9278	bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster	Neurohypophysis enriched cells	5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.	5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.	37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.	strain:AB Tgpomca:EGFP\|tissue:Neurohypophysis\|age:7 month	GSM6153483	GSM6153483: AB9278; Danio rerio; RNA Seq	GSM6153483 r1	GSM6153483	1	5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP375342	loader:fastq load.py	AB9278_SB390_R1_01.fastq.gz AB9278_SB390_R2_01.fastq.gz	fastq fastq	1259447780.0	11770540.0	GSM6153483 r1	0:92 1:15	A:305608913;C:313550706;G:363197186;T:277079546;N:11429	92	15	305608913	313550706	363197186	277079546	11429	SRX15281308	SRS13012753	SRA1420605	Molecular Cell Biology, Weizmann Institute of Science	Molecular Cell Biology, Weizmann Institute of Science	2	0.94767	0.32091	0.89796	1.0	0.7545	92	15	B	T	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-05-16	Adult	Adult	Pituitary Gland	Endocrine System
69989	69989	SRR19217300	SRX15281307	SRS13012752	SRP375342	PRJNA838481	Neural plate progenitors give rise to both anterior and posterior pituitary cells	GSE203075	Transcriptome Analysis	The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.	pubmed:37683631	AB9277	GSM6153482	source name:Neurohypophysis enriched cells\|strain:AB Tgpomca:EGFP\|tissue:Neurohypophysis\|age:7 month\|geo loc name:missing\|collection date:missing	AB9277	bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster	Neurohypophysis enriched cells	5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.	5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.	37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.	strain:AB Tgpomca:EGFP\|tissue:Neurohypophysis\|age:7 month	GSM6153482	GSM6153482: AB9277; Danio rerio; RNA Seq	GSM6153482 r1	GSM6153482	1	5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP375342	loader:fastq load.py	AB9277_SB390_R1_01.fastq.gz AB9277_SB390_R2_01.fastq.gz	fastq fastq	1130776107.0	10568001.0	GSM6153482 r1	0:92 1:15	A:288600700;C:269726443;G:310844405;T:261594352;N:10207	92	15	288600700	269726443	310844405	261594352	10207	SRX15281307	SRS13012752	SRA1420605	Molecular Cell Biology, Weizmann Institute of Science	Molecular Cell Biology, Weizmann Institute of Science	2	0.94379	0.28638	0.86415	1.0	0.63321	92	15	B	T	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-05-16	Adult	Adult	Pituitary Gland	Endocrine System
69990	69990	SRR19217301	SRX15281306	SRS13012751	SRP375342	PRJNA838481	Neural plate progenitors give rise to both anterior and posterior pituitary cells	GSE203075	Transcriptome Analysis	The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.	pubmed:37683631	AB9280	GSM6153481	source name:Neurohypophysis enriched cells\|strain:AB Tgpomca:EGFP\|tissue:Neurohypophysis\|age:5 month\|geo loc name:missing\|collection date:missing	AB9280	bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster	Neurohypophysis enriched cells	5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.	5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.	37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.	strain:AB Tgpomca:EGFP\|tissue:Neurohypophysis\|age:5 month	GSM6153481	GSM6153481: AB9280; Danio rerio; RNA Seq	GSM6153481 r1	GSM6153481	1	5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP375342	loader:fastq load.py	AB9280_SB390_R1_01.fastq.gz AB9280_SB390_R2_01.fastq.gz	fastq fastq	1172966528.0	10962304.0	GSM6153481 r1	0:92 1:15	A:311089180;C:274626206;G:310304031;T:276936052;N:11059	92	15	311089180	274626206	310304031	276936052	11059	SRX15281306	SRS13012751	SRA1420605	Molecular Cell Biology, Weizmann Institute of Science	Molecular Cell Biology, Weizmann Institute of Science	2	0.92936	0.23628	0.86147	1.0	0.74656	92	15	B	T	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-05-16	Adult	Adult	Pituitary Gland	Endocrine System
69991	69991	SRR19217302	SRX15281305	SRS13012750	SRP375342	PRJNA838481	Neural plate progenitors give rise to both anterior and posterior pituitary cells	GSE203075	Transcriptome Analysis	The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.	pubmed:37683631	AB9279	GSM6153480	source name:Neurohypophysis enriched cells\|strain:AB Tgpomca:EGFP\|tissue:Neurohypophysis\|age:5 month\|geo loc name:missing\|collection date:missing	AB9279	bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster	Neurohypophysis enriched cells	5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.	5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.	37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.	strain:AB Tgpomca:EGFP\|tissue:Neurohypophysis\|age:5 month	GSM6153480	GSM6153480: AB9279; Danio rerio; RNA Seq	GSM6153480 r1	GSM6153480	1	5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP375342	loader:fastq load.py	AB9279_SB390_R1_01.fastq.gz AB9279_SB390_R2_01.fastq.gz	fastq fastq	1383147163.0	12926609.0	GSM6153480 r1	0:92 1:15	A:364575971;C:320901229;G:367626618;T:330030659;N:12686	92	15	364575971	320901229	367626618	330030659	12686	SRX15281305	SRS13012750	SRA1420605	Molecular Cell Biology, Weizmann Institute of Science	Molecular Cell Biology, Weizmann Institute of Science	2	0.92462	0.26743	0.8493	1.0	0.74133	92	15	B	T	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-05-16	Adult	Adult	Pituitary Gland	Endocrine 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");;