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
33348,SRR30085223,SRX25558689,SRS22210797,SRP523634,PRJNA1142970,rna sequncing of POMC miR 7a zebrafish,PRJNA1142970,Other,,,,,,Pomc WT,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:5 mpf date:2017 03|geo loc name:Taiwan|sex:pooled male and female|tissue:Pituitary gland|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of pomc neuron:wild type zebrafish,Pomc WT,Pomc WT,RNA was extracted from pooled zebrafish pomc neron,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiScanSQ,,SRP523634,,,Pomc_WT_1.fq Pomc_WT_2.fq,fastq fastq,7525490700.0,25084969.0,Pomc WT 1.fq,0:150 1:150,A:2000028813;C:1750437540;G:1771219215;T:2003249941;N:555191,150,150,,,2000028813,1750437540,1771219215,2003249941,555191,SRX25558689,SRS22210797,SRA1937807,National Yang Ming Chiao Tung University|Institute of Biopharmaceutical Sciences,National Yang Ming Chiao Tung University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Taiwan,2024-08-01,Adult,Adult,Pituitary Gland,Endocrine System
33349,SRR30085224,SRX25558688,SRS22210796,SRP523634,PRJNA1142970,rna sequncing of POMC miR 7a zebrafish,PRJNA1142970,Other,,,,,,Pomc 7a,,strain:Pomc miR7a|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:5 mpf date:2017 03|geo loc name:Taiwan|sex:pooled male and female|tissue:Pituitary gland|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of pomc neuron:micorRNA 7a overexpressed zebrafish,Pomc 7a,Pomc 7a,RNA was extracted from pooled zebrafish pomc neron,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiScanSQ,,SRP523634,,,Pomc_7a_1.fq Pomc_7a_2.fq,fastq fastq,9785072700.0,32616909.0,Pomc 7a 1.fq,0:150 1:150,A:2643936280;C:2244968340;G:2260302975;T:2635083506;N:781599,150,150,,,2643936280,2244968340,2260302975,2635083506,781599,SRX25558688,SRS22210796,SRA1937807,National Yang Ming Chiao Tung University|Institute of Biopharmaceutical Sciences,National Yang Ming Chiao Tung University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Taiwan,2024-08-01,Adult,Adult,Pituitary Gland,Endocrine System
44043,SRR6237746,SRX3345984,SRS2646512,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate2 A6 AMCA,GSM2836694,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,Sample Plate2 A6 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,GSM2836694,GSM2836694: Sample Plate2 A6 AMCA; Danio rerio; RNA Seq,GSM2836694,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836694,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate2_A6_AMCA_Neg.fastq.gz,fastq,1229895822.0,20184545.0,GSM2836694 r1,0:60.93 1:0,A:354923207;C:259144918;G:256606445;T:359057403;N:163849,60,0,,,354923207,259144918,256606445,359057403,163849,SRX3345984,SRS2646512,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.87646,,0.26527,,0.8257,,0.55303,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44044,SRR6237745,SRX3345983,SRS2646515,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate2 A5 AMCA,GSM2836693,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,Sample Plate2 A5 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,GSM2836693,GSM2836693: Sample Plate2 A5 AMCA; Danio rerio; RNA Seq,GSM2836693,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836693,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate2_A5_AMCA_Pos.fastq.gz,fastq,925676587.0,15189171.0,GSM2836693 r1,0:60.94 1:0,A:282028510;C:179853567;G:179383383;T:284281435;N:129692,60,0,,,282028510,179853567,179383383,284281435,129692,SRX3345983,SRS2646515,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.90747,,0.36422,,0.74215,,0.54419,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44045,SRR6237744,SRX3345982,SRS2646511,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate2 A4 AMCA,GSM2836692,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,Sample Plate2 A4 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,GSM2836692,GSM2836692: Sample Plate2 A4 AMCA; Danio rerio; RNA Seq,GSM2836692,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836692,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate2_A4_AMCA_Neg.fastq.gz,fastq,1160014329.0,19037174.0,GSM2836692 r1,0:60.93 1:0,A:339245851;C:240318483;G:237965388;T:342331066;N:153541,60,0,,,339245851,240318483,237965388,342331066,153541,SRX3345982,SRS2646511,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.89175,,0.24416,,0.82384,,0.55389,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44046,SRR6237743,SRX3345981,SRS2646513,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate2 A3 AMCA,GSM2836691,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,Sample Plate2 A3 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,GSM2836691,GSM2836691: Sample Plate2 A3 AMCA; Danio rerio; RNA Seq,GSM2836691,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836691,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate2_A3_AMCA_Pos.fastq.gz,fastq,855655864.0,14040472.0,GSM2836691 r1,0:60.94 1:0,A:257233140;C:169854422;G:169238352;T:259211059;N:118891,60,0,,,257233140,169854422,169238352,259211059,118891,SRX3345981,SRS2646513,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.90605,,0.30761,,0.74067,,0.55271,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44047,SRR6237742,SRX3345980,SRS2646514,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate2 A2 AMCA,GSM2836690,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,Sample Plate2 A2 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,GSM2836690,GSM2836690: Sample Plate2 A2 AMCA; Danio rerio; RNA Seq,GSM2836690,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836690,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate2_A2_AMCA_Neg.fastq.gz,fastq,1168909471.0,19185392.0,GSM2836690 r1,0:60.93 1:0,A:326281148;C:256738933;G:252744782;T:332989234;N:155374,60,0,,,326281148,256738933,252744782,332989234,155374,SRX3345980,SRS2646514,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.88849,,0.1697,,0.86602,,0.52913,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44048,SRR6237741,SRX3345979,SRS2646510,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate2 A1 AMCA,GSM2836689,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,Sample Plate2 A1 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,GSM2836689,GSM2836689: Sample Plate2 A1 AMCA; Danio rerio; RNA Seq,GSM2836689,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836689,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate2_A1_AMCA_Pos.fastq.gz,fastq,915106129.0,15016536.0,GSM2836689 r1,0:60.94 1:0,A:271804923;C:184830364;G:184695096;T:273646193;N:129553,60,0,,,271804923,184830364,184695096,273646193,129553,SRX3345979,SRS2646510,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.909,,0.28209,,0.74582,,0.54537,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44049,SRR6237740,SRX3345978,SRS2646509,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate1 A8 AMCA,GSM2836688,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,Sample Plate1 A8 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,GSM2836688,GSM2836688: Sample Plate1 A8 AMCA; Danio rerio; RNA Seq,GSM2836688,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836688,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate1_A8_AMCA_Neg.fastq.gz,fastq,1174636209.0,19276749.0,GSM2836688 r1,0:60.94 1:0,A:346218731;C:240547553;G:237863913;T:349847274;N:158738,60,0,,,346218731,240547553,237863913,349847274,158738,SRX3345978,SRS2646509,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.89653,,0.29731,,0.82388,,0.57688,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44050,SRR6237739,SRX3345977,SRS2646507,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate1 A7 AMCA,GSM2836687,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,Sample Plate1 A7 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,GSM2836687,GSM2836687: Sample Plate1 A7 AMCA; Danio rerio; RNA Seq,GSM2836687,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836687,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate1_A7_AMCA_Pos.fastq.gz,fastq,919004945.0,15079582.0,GSM2836687 r1,0:60.94 1:0,A:281188323;C:177657384;G:177254638;T:282775426;N:129174,60,0,,,281188323,177657384,177254638,282775426,129174,SRX3345977,SRS2646507,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.8999,,0.31855,,0.7643,,0.56856,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44051,SRR6237738,SRX3345976,SRS2646506,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate1 A6 AMCA,GSM2836686,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,Sample Plate1 A6 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes,GSM2836686,GSM2836686: Sample Plate1 A6 AMCA; Danio rerio; RNA Seq,GSM2836686,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836686,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate1_A6_AMCA_Neg.fastq.gz,fastq,1217567270.0,19981819.0,GSM2836686 r1,0:60.93 1:0,A:366468588;C:242252329;G:239380324;T:369298417;N:167612,60,0,,,366468588,242252329,239380324,369298417,167612,SRX3345976,SRS2646506,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.87327,,0.29592,,0.86026,,0.61414,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44052,SRR6237737,SRX3345975,SRS2646508,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate1 A5 AMCA,GSM2836685,,source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,Sample Plate1 A5 AMCA,cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2,hypophysis,Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,Adult zebrafish were raised and bred according to standard protocols.,strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes,GSM2836685,GSM2836685: Sample Plate1 A5 AMCA; Danio rerio; RNA Seq,GSM2836685,,1,Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80°C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.,GEO Accession:GSM2836685,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP123109,,,Sample_Plate1_A5_AMCA_Pos.fastq.gz,fastq,995781320.0,16339491.0,GSM2836685 r1,0:60.94 1:0,A:304872127;C:192446811;G:191928153;T:306392280;N:141949,60,0,,,304872127,192446811,191928153,306392280,141949,SRX3345975,SRS2646508,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.90464,,0.36217,,0.74836,,0.56177,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
55229,SRR10199493,SRX6919651,SRS5450537,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23PG replicate 1,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:15 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,CHR23 PG1,CHR23 PG1,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-PG1_combined_R1.fastq.gz Chr23-PG1_combined_R2.fastq.gz,fastq fastq,6654002100.0,22180007.0,Chr23 PG1 combined R1.fastq.gz,0:150 1:150,A:1819739632;C:1499478529;G:1515944103;T:1818620794;N:219042,150,150,,,1819739632,1499478529,1515944103,1818620794,219042,SRX6919651,SRS5450537,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.92113,0.92255,0.09207,0.09331,0.71573,0.7205,0.52726,0.58205,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55241,SRR10199505,SRX6919639,SRS5450525,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTPG replicate 3,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:20 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,WT PG3,WT PG3,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-PG3_combined_R1.fastq.gz WT-PG3_combined_R2.fastq.gz,fastq fastq,6751713000.0,22505710.0,WT PG3 combined R1.fastq.gz,0:150 1:150,A:1869416559;C:1496572806;G:1514851553;T:1870652394;N:219688,150,150,,,1869416559,1496572806,1514851553,1870652394,219688,SRX6919639,SRS5450525,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.92953,0.93151,0.09098,0.09156,0.73074,0.73699,0.66993,0.67339,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55242,SRR10199506,SRX6919638,SRS5450524,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTPG replicate 2,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:19 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,WT PG2,WT PG2,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-PG2_combined_R1.fastq.gz WT-PG2_combined_R2.fastq.gz,fastq fastq,6370809600.0,21236032.0,WT PG2 combined R1.fastq.gz,0:150 1:150,A:1787150048;C:1388750804;G:1405374191;T:1789322231;N:212326,150,150,,,1787150048,1388750804,1405374191,1789322231,212326,SRX6919638,SRS5450524,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.9274,0.92797,0.09768,0.09788,0.7288,0.73387,0.6714,0.67474,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55243,SRR10199507,SRX6919637,SRS5450523,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTPG replicate 1,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:18 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,WT PG1,WT PG1,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-PG1_combined_R1.fastq.gz WT-PG1_combined_R2.fastq.gz,fastq fastq,7088374200.0,23627914.0,WT PG1 combined R1.fastq.gz,0:150 1:150,A:1976454953;C:1556957648;G:1576097593;T:1978627198;N:236808,150,150,,,1976454953,1556957648,1576097593,1978627198,236808,SRX6919637,SRS5450523,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.92813,0.92862,0.09435,0.09468,0.73072,0.73732,0.67177,0.67649,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55244,SRR10199508,SRX6919636,SRS5450522,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23PG replicate 3,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:17 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,CHR23 PG3,CHR23 PG3,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-PG3_combined_R1.fastq.gz Chr23-PG3_combined_R2.fastq.gz,fastq fastq,6306831900.0,21022773.0,Chr23 PG3 combined R1.fastq.gz,0:150 1:150,A:1761625771;C:1384630771;G:1399189529;T:1761175818;N:210011,150,150,,,1761625771,1384630771,1399189529,1761175818,210011,SRX6919636,SRS5450522,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.91822,0.91897,0.09779,0.09773,0.71676,0.72198,0.59874,0.52969,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55245,SRR10199509,SRX6919635,SRS5450521,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23PG replicate 2,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:16 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,CHR23 PG2,CHR23 PG2,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-PG2_combined_R1.fastq.gz Chr23-PG2_combined_R2.fastq.gz,fastq fastq,6790899600.0,22636332.0,Chr23 PG2 combined R1.fastq.gz,0:150 1:150,A:1842525837;C:1545697169;G:1560457672;T:1841998398;N:220524,150,150,,,1842525837,1545697169,1560457672,1841998398,220524,SRX6919635,SRS5450521,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.92407,0.92584,0.0916,0.09113,0.71644,0.72141,0.5239,0.59097,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
58918,SRR11540947,SRX8111243,SRS6476317,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Transplant,GSM4474605,,source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month,Transplant,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month,GSM4474605,GSM4474605: Transplant; Danio rerio; RNA Seq,GSM4474605,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474605,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,ubieGFP_Pit-Endo-transp_3mpf-m-1_S25_L001_R2_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-1_S25_L001_R1_001.fastq.gz,fastq fastq,32025333121.0,217126081.0,GSM4474605 r1,0:27 1:120.50,A:9314654962;C:6522735572;G:6826173512;T:9343095148;N:18673927,27,120,,,9314654962,6522735572,6826173512,9343095148,18673927,SRX8111243,SRS6476317,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00161,0.90845,0.00057,0.11751,0.99687,0.82771,0.47738,0.59877,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58919,SRR11540948,SRX8111243,SRS6476317,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Transplant,GSM4474605,,source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month,Transplant,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month,GSM4474605,GSM4474605: Transplant; Danio rerio; RNA Seq,GSM4474605,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474605,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,ubieGFP_Pit-Endo-transp_3mpf-m-2_S26_L001_R1_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-2_S26_L001_R2_001.fastq.gz,fastq fastq,37830323844.0,256490571.0,GSM4474605 r2,0:27 1:120.49,A:11021068490;C:7699701868;G:8072819621;T:11014855601;N:21878264,27,120,,,11021068490,7699701868,8072819621,11014855601,21878264,SRX8111243,SRS6476317,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00167,0.90711,0.00066,0.11917,0.99663,0.83,0.53886,0.59796,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58920,SRR11540949,SRX8111243,SRS6476317,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Transplant,GSM4474605,,source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month,Transplant,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month,GSM4474605,GSM4474605: Transplant; Danio rerio; RNA Seq,GSM4474605,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474605,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,ubieGFP_Pit-Endo-transp_3mpf-m-3_S27_L001_R2_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-3_S27_L001_R1_001.fastq.gz,fastq fastq,28249532732.0,191530324.0,GSM4474605 r3,0:27 1:120.49,A:8193419181;C:5751619572;G:6039589822;T:8248615264;N:16288893,27,120,,,8193419181,5751619572,6039589822,8248615264,16288893,SRX8111243,SRS6476317,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.0017,0.90552,0.0006,0.11697,0.99667,0.82576,0.54976,0.60065,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58921,SRR11540950,SRX8111243,SRS6476317,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Transplant,GSM4474605,,source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month,Transplant,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month,GSM4474605,GSM4474605: Transplant; Danio rerio; RNA Seq,GSM4474605,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474605,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,ubieGFP_Pit-Endo-transp_3mpf-m-4_S28_L001_R2_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-4_S28_L001_R1_001.fastq.gz,fastq fastq,28226688209.0,191373742.0,GSM4474605 r4,0:27 1:120.50,A:8176659734;C:5765390596;G:6034905304;T:8233376515;N:16356060,27,120,,,8176659734,5765390596,6034905304,8233376515,16356060,SRX8111243,SRS6476317,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00163,0.90646,0.00056,0.11667,0.99667,0.82603,0.57,0.59607,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58922,SRR11540943,SRX8111242,SRS6476316,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Male1,GSM4474604,,source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,Male1,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,GSM4474604,GSM4474604: Male1; Danio rerio; RNA Seq,GSM4474604,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474604,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,M1_Pituitary_Sox17creERUbiGtR-1_S13_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-1_S13_L001_R1_001.fastq.gz,fastq fastq,31605717037.0,214359798.0,GSM4474604 r1,0:27 1:120.44,A:9104842871;C:6521304311;G:6857625119;T:9101526427;N:20418309,27,120,,,9104842871,6521304311,6857625119,9101526427,20418309,SRX8111242,SRS6476316,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00259,0.88483,0.00097,0.20321,0.995,0.80079,0.52597,0.56862,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58923,SRR11540944,SRX8111242,SRS6476316,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Male1,GSM4474604,,source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,Male1,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,GSM4474604,GSM4474604: Male1; Danio rerio; RNA Seq,GSM4474604,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474604,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,M1_Pituitary_Sox17creERUbiGtR-2_S14_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-2_S14_L001_R1_001.fastq.gz,fastq fastq,27674233334.0,187694200.0,GSM4474604 r2,0:27 1:120.44,A:7958817473;C:5737419593;G:6003046001;T:7957045184;N:17905083,27,120,,,7958817473,5737419593,6003046001,7957045184,17905083,SRX8111242,SRS6476316,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00275,0.88312,0.00108,0.20427,0.99478,0.80608,0.47634,0.56166,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58924,SRR11540945,SRX8111242,SRS6476316,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Male1,GSM4474604,,source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,Male1,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,GSM4474604,GSM4474604: Male1; Danio rerio; RNA Seq,GSM4474604,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474604,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,M1_Pituitary_Sox17creERUbiGtR-3_S15_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-3_S15_L001_R1_001.fastq.gz,fastq fastq,35522886586.0,240929767.0,GSM4474604 r3,0:27 1:120.44,A:10224992422;C:7358725736;G:7719740991;T:10196515119;N:22912318,27,120,,,10224992422,7358725736,7719740991,10196515119,22912318,SRX8111242,SRS6476316,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.0028,0.88842,0.00103,0.20371,0.99468,0.80127,0.46449,0.4682,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58925,SRR11540946,SRX8111242,SRS6476316,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Male1,GSM4474604,,source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,Male1,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,GSM4474604,GSM4474604: Male1; Danio rerio; RNA Seq,GSM4474604,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474604,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,M1_Pituitary_Sox17creERUbiGtR-4_S16_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-4_S16_L001_R1_001.fastq.gz,fastq fastq,22322824317.0,151402860.0,GSM4474604 r4,0:27 1:120.44,A:6438472506;C:4603208282;G:4838569546;T:6428191408;N:14382575,27,120,,,6438472506,4603208282,4838569546,6428191408,14382575,SRX8111242,SRS6476316,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00247,0.88259,0.00091,0.20556,0.99521,0.80395,0.47651,0.55966,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58926,SRR11540939,SRX8111241,SRS6476315,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Males,GSM4474603,,source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,Males,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,GSM4474603,GSM4474603: Males; Danio rerio; RNA Seq,GSM4474603,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474603,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,M_Pituitary_Sox17creERUbiGtR-1_S9_L001_R1_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-1_S9_L001_R2_001.fastq.gz,fastq fastq,47824931084.0,324315726.0,GSM4474603 r1,0:27 1:120.46,A:13805207199;C:9886339394;G:10399128349;T:13703273256;N:30982886,27,120,,,13805207199,9886339394,10399128349,13703273256,30982886,SRX8111241,SRS6476315,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00277,0.89029,0.00096,0.16996,0.99462,0.81481,0.49279,0.59136,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58927,SRR11540940,SRX8111241,SRS6476315,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Males,GSM4474603,,source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,Males,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,GSM4474603,GSM4474603: Males; Danio rerio; RNA Seq,GSM4474603,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474603,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,M_Pituitary_Sox17creERUbiGtR-2_S10_L001_R2_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-2_S10_L001_R1_001.fastq.gz,fastq fastq,32243370700.0,218650680.0,GSM4474603 r2,0:27 1:120.47,A:9305381092;C:6663053359;G:7018746988;T:9235440820;N:20748441,27,120,,,9305381092,6663053359,7018746988,9235440820,20748441,SRX8111241,SRS6476315,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00277,0.8884,0.00091,0.1672,0.99458,0.81533,0.51123,0.58754,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58928,SRR11540941,SRX8111241,SRS6476315,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Males,GSM4474603,,source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,Males,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,GSM4474603,GSM4474603: Males; Danio rerio; RNA Seq,GSM4474603,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474603,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,M_Pituitary_Sox17creERUbiGtR-3_S11_L001_R1_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-3_S11_L001_R2_001.fastq.gz,fastq fastq,28915149568.0,196083542.0,GSM4474603 r3,0:27 1:120.46,A:8347281799;C:5984386507;G:6301924708;T:8262927533;N:18629021,27,120,,,8347281799,5984386507,6301924708,8262927533,18629021,SRX8111241,SRS6476315,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00281,0.88705,0.00088,0.16827,0.99454,0.81233,0.49184,0.58837,27,118,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System
58929,SRR11540942,SRX8111241,SRS6476315,SRP256300,PRJNA625098,Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary,GSE148591,Transcriptome Analysis,Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.,,pubmed:33093109,,Males,GSM4474603,,source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,Males,10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files,Pituitary,,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,6mpf animals Males and Male1 and 3mpf animal for transplant,genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month,GSM4474603,GSM4474603: Males; Danio rerio; RNA Seq,GSM4474603,,1,Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.,GEO Accession:GSM4474603,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP256300,,,M_Pituitary_Sox17creERUbiGtR-4_S12_L001_R2_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-4_S12_L001_R1_001.fastq.gz,fastq fastq,33158543550.0,224853573.0,GSM4474603 r4,0:27 1:120.47,A:9576940269;C:6855014912;G:7203590871;T:9501520990;N:21476508,27,120,,,9576940269,6855014912,7203590871,9501520990,21476508,SRX8111241,SRS6476315,SRA1065111,GEO,"Crump Lab, Stem Cell, USC",2,0.00273,0.8878,0.00089,0.16918,0.99494,0.81801,0.51694,0.58973,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2020-04-13,Adult,Adult,Pituitary Gland,Endocrine System