run_metadata: 34930

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
34930	SRR32424870	SRX27754015	SRS24139546	SRP565442	PRJNA1226487	Separate brainstem circuits for fast steering and slow exploratory turns	GSE290157	Transcriptome Analysis	During locomotion trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change rather than the locomotor frequency. The brainstem steering neurons are in turn controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg gly2: GFP zebrafish brain stem one cell from each fish a total of eight fish				Glycinergic neurons m5	GSM8807150		tissue:Glycinergic neurons\|cell type:Glycinergic neurons\|genotype:Tg gly2: GFP\|geo loc name:missing\|collection date:missing	Glycinergic neurons m5	Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.	Glycinergic neurons		RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.		cell type:Glycinergic neurons\|genotype:Tg gly2: GFP	GSM8807150	GSM8807150: Glycinergic neurons m5; Danio rerio; RNA Seq	GSM8807150 r1	GSM8807150	1	RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA Inc. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP565442			M5_1.fq.gz M5_2.fq.gz	fastq fastq	8381104622.0	30664708.0	GSM8807150 r1		A:2289409726;C:1427540731;G:1492945660;T:3168884923;N:2323582					2289409726	1427540731	1492945660	3168884923	2323582	SRX27754015	SRS24139546	SRA2081247	TongJi university	TongJi university												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq		China	2025-02-21	Undetermined	Undetermined	Brain	Nervous System