{"database": "metadata", "table": "run_metadata", "rows": [[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", null, "pubmed:30449506", null, "Sample Plate2 A5 AMCA", "GSM2836693", null, "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 \u03b2 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 250\u00b5L 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 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C 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 \u03bcm 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 70\u00b5m 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\u00b0C. 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\u00ae Ultra\u2122 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", null, "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 250\u00b5L 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 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C 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 \u03bcm 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 70\u00b5m 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\u00b0C. 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\u00ae Ultra\u2122 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", null, "SRP123109", null, null, "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, null, null, 282028510, 179853567, 179383383, 284281435, 129692, "SRX3345983", "SRS2646515", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.90747, null, 0.36422, null, 0.74215, null, 0.54419, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["44044"], "units": {}, "query_ms": 10.141343002032954}