run_metadata: 45060

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
45060	SRR6497182	SRX3586251	SRS2608614	SRP131047	PRJNA429936	10X genomics analysis of adult and larval habenula from the gng8 GFP transgenic line	GSE109158	Transcriptome Analysis	The identification of cell types and marker genes is critical for dissecting neural development and function but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly despite brain growth and functional maturation cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: For larval dataset multiple gng8 GFP labeled zebrafish brains were dissociated and habenular cells FAC sorted into PBS+1%BSA and immediately loaded into 10X chromium for cell capture. For adult dataset 5 6 habenulae were cleanly dissected out dissociated filtered in PBS+BSA and immediately captured in droplets with 10x platform. Both libraries were then constructed using standard instrutions of the 10x plaform.	parent bioproject:PRJNA414719	pubmed:29576475		HabenulaR1	GSM2818522		source name:adult habenula\|developmental stage:Adult\|tissue:Brain\|tissue subtype:adult habenula	HabenulaR1	Raw requencing data was converted to matrizes of expression conts using cell ranger software provided by 10x genomics. Briefly raw BCL files from Illumina nExtseq were demultiplexed into compressed Fastqs for each channel using "cellranger mkfastq" FASTQ files were then provided as input to “cellranger count” which partitioned the reads into their cell of origin based on the 14bp cell barcode on the left read aligned reads to a zebrafish reference transcriptome and quantified transcript counts for each annotated gene within every cell. Here the 10bp unique molecular identifier UMI on the left read was used to collapse PCR duplicates and accurately quantify the number of transcript molecules captured for each gene in every cell. Supplementary files format and content: text file with tab delimiters	adult habenula		polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/		developmental stage:Adult\|tissue:Brain\|tissue subtype:adult habenula	GSM2818522	GSM2818522: HabenulaR1; Danio rerio; RNA Seq	GSM2818522 2		1	polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/	GEO Accession:GSM2818522	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP131047			AdultR1_possorted_genome_bam.bam dr82_jeffspike.fasta	10X Genomics bam file fasta	34221168849.0	580019811.0	GSM2818522 r11	0:59	A:10793327710;C:6125333298;G:6353453321;T:10947283926;N:1770594	59				10793327710	6125333298	6353453321	10947283926	1770594	SRX3586251	SRS2608614	SRA650466	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	1	0.84773		0.23824		0.816		0.51567		59		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x		United States	2017-10-18	Adult	Adult	Brain	Nervous System