run_metadata: 74200

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
74200	SRR23592282	SRX19477371	SRS16868714	SRP424004	PRJNA937732	Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution	GSE225863	Transcriptome Analysis	The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.		pubmed:38518783		Replicate2	GSM7058865		source name:Telencephalon\|tissue:Telencephalon\|genotype:TgSox2:gfp\|age:12 weeks	Replicate2	The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Telencephalon		Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		tissue:Telencephalon\|genotype:TgSox2:gfp\|age:12 weeks	GSM7058865	GSM7058865: Replicate2; Danio rerio; RNA Seq	GSM7058865 r1	GSM7058865	1	Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP424004		loader:fastq load.py	Replicate2_S4_L008_I1_001.fastq.gz Replicate2_S4_L008_R1_001.fastq.gz Replicate2_S4_L008_R2_001.fastq.gz	fastq fastq fastq	9442724016.0	71535788.0	GSM7058865 r7	0:8 1:26 2:98	A:2101696435;C:1327881205;G:1415404738;T:2163690490;N:1834356	8	26	98		2101696435	1327881205	1415404738	2163690490	1834356	SRX19477371	SRS16868714	SRA1594515	Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur	Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur	1	0.87989		0.29895		0.7668		0.50886		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x		France	2023-02-22	Juvenile	Juvenile	Brain	Nervous System