run_metadata: 44045

This data as json

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
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