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.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,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.spot_descriptor,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.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.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,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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",2,0.94767,0.0,0.32091,0.0,0.89796,1.0,0.7545,,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,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",2,0.94379,0.0,0.28638,0.0,0.86415,1.0,0.63321,,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,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",2,0.92936,0.0,0.23628,0.0,0.86147,1.0,0.74656,,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,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",2,0.92462,0.0,0.26743,0.0,0.8493,1.0,0.74133,,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
69992,SRR19217303,SRX15281304,SRS13012749,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,,AB7418,GSM6153479,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing,AB7418,"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:37 dpf,GSM6153479,GSM6153479: AB7418; Danio rerio; RNA Seq,GSM6153479 r1,GSM6153479,1,5 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,,,AB7418_SB350_S35_R1_001.fastq.gz AB7418_SB350_S35_R2_001.fastq.gz,fastq fastq,2468773944.0,29390166.0,GSM6153479 r1,0:69 1:15,A:764359919;C:520031317;G:592699381;T:591594655;N:88672,69,15,,,764359919,520031317,592699381,591594655,88672,SRX15281304,SRS13012749,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.85786,0.0,0.15143,0.0,0.84885,1.0,0.67021,,69,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Juvenile,Juvenile,Pituitary Gland,Endocrine System
69993,SRR19217304,SRX15281303,SRS13012748,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,,AB7417,GSM6153478,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing,AB7417,"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:37 dpf,GSM6153478,GSM6153478: AB7417; Danio rerio; RNA Seq,GSM6153478 r1,GSM6153478,1,5 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,,,AB7417_SB350_S24_R1_001.fastq.gz AB7417_SB350_S24_R2_001.fastq.gz,fastq fastq,2586526488.0,30791982.0,GSM6153478 r1,0:69 1:15,A:833353097;C:525447349;G:601496569;T:626135990;N:93483,69,15,,,833353097,525447349,601496569,626135990,93483,SRX15281303,SRS13012748,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.84125,0.0,0.10717,0.0,0.84768,1.0,0.63154,,69,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Juvenile,Juvenile,Pituitary Gland,Endocrine System