run_metadata: 58920

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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
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